1
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Augustijnen H, Lucek K. Beyond gene flow: (non)-parallelism of secondary contact in a pair of highly differentiated sibling species. Mol Ecol 2024; 33:e17488. [PMID: 39119885 DOI: 10.1111/mec.17488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/01/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024]
Abstract
Replicated secondary contact zones can provide insights into the barriers to gene flow that are important during speciation and can reveal to which degree secondary contact may result in similar evolutionary outcomes. Here, we studied two secondary contact zones between highly differentiated Alpine butterflies of the genus Erebia using whole-genome resequencing data. We assessed the genomic relationships between populations and species and found hybridization to be rare, with no to little current or historical introgression in either contact zone. There are large similarities between contact zones, consistent with an allopatric origin of interspecific differentiation, with no indications for ongoing reinforcing selection. Consistent with expected reduced effective population size, we further find that scaffolds related to the Z-chromosome show increased differentiation compared to the already high levels across the entire genome, which could also hint towards a contribution of the Z chromosome to species divergence in this system. Finally, we detected the presence of the endosymbiont Wolbachia, which can cause reproductive isolation between its hosts, in all E. cassioides, while it appears to be fully or largely absent in contact zone populations of E. tyndarus. We discuss how this rare pattern may have arisen and how it may have affected the dynamics of speciation upon secondary contact.
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Affiliation(s)
- Hannah Augustijnen
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Kay Lucek
- Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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2
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Rueda-M N, Pardo-Diaz C, Montejo-Kovacevich G, McMillan WO, Kozak KM, Arias CF, Ready J, McCarthy S, Durbin R, Jiggins CD, Meier JI, Salazar C. Genomic evidence reveals three W-autosome fusions in Heliconius butterflies. PLoS Genet 2024; 20:e1011318. [PMID: 39024186 PMCID: PMC11257349 DOI: 10.1371/journal.pgen.1011318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/24/2024] [Indexed: 07/20/2024] Open
Abstract
Sex chromosomes are evolutionarily labile in many animals and sometimes fuse with autosomes, creating so-called neo-sex chromosomes. Fusions between sex chromosomes and autosomes have been proposed to reduce sexual conflict and to promote adaptation and reproductive isolation among species. Recently, advances in genomics have fuelled the discovery of such fusions across the tree of life. Here, we discovered multiple fusions leading to neo-sex chromosomes in the sapho subclade of the classical adaptive radiation of Heliconius butterflies. Heliconius butterflies generally have 21 chromosomes with very high synteny. However, the five Heliconius species in the sapho subclade show large variation in chromosome number ranging from 21 to 60. We find that the W chromosome is fused with chromosome 4 in all of them. Two sister species pairs show subsequent fusions between the W and chromosomes 9 or 14, respectively. These fusions between autosomes and sex chromosomes make Heliconius butterflies an ideal system for studying the role of neo-sex chromosomes in adaptive radiations and the degeneration of sex chromosomes over time. Our findings emphasize the capability of short-read resequencing to detect genomic signatures of fusion events between sex chromosomes and autosomes even when sex chromosomes are not explicitly assembled.
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Affiliation(s)
- Nicol Rueda-M
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Carolina Pardo-Diaz
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | | | - Krzysztof M. Kozak
- Smithsonian Tropical Research Institute, Panama City, Panama
- Museum of Vertebrate Zoology, Berkeley, California, United States of America
| | - Carlos F. Arias
- Smithsonian Tropical Research Institute, Panama City, Panama
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, Washington DC, United States of America
| | - Jonathan Ready
- Institute for Biological Sciences, Federal University of Pará - UFPA, Belém, Brazil
- Centre for Advanced Studies of Biodiversity - CEABIO, Belém, Brazil
| | - Shane McCarthy
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Richard Durbin
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Joana I. Meier
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
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3
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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. SCIENCE ADVANCES 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] [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.
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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
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4
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Thom G, Moreira LR, Batista R, Gehara M, Aleixo A, Smith BT. Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds. Genome Biol Evol 2024; 16:evae002. [PMID: 38236173 PMCID: PMC10823491 DOI: 10.1093/gbe/evae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/26/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how variation in genomic characteristics (e.g. recombination rate) impacts our ability to reconstruct general patterns of differentiation between species that cooccur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in genomic regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations toward lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate spatial patterns of population differentiation.
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Affiliation(s)
- Gregory Thom
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Lucas Rocha Moreira
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Romina Batista
- Programa de Coleções Biológicas, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
- School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Department of Environmental Genomics, Instituto Tecnológico Vale, Belém, Brazil
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
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5
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Thawornwattana Y, Seixas F, Yang Z, Mallet J. Major patterns in the introgression history of Heliconius butterflies. eLife 2023; 12:RP90656. [PMID: 38108819 PMCID: PMC10727504 DOI: 10.7554/elife.90656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
Gene flow between species, although usually deleterious, is an important evolutionary process that can facilitate adaptation and lead to species diversification. It also makes estimation of species relationships difficult. Here, we use the full-likelihood multispecies coalescent (MSC) approach to estimate species phylogeny and major introgression events in Heliconius butterflies from whole-genome sequence data. We obtain a robust estimate of species branching order among major clades in the genus, including the 'melpomene-silvaniform' group, which shows extensive historical and ongoing gene flow. We obtain chromosome-level estimates of key parameters in the species phylogeny, including species divergence times, present-day and ancestral population sizes, as well as the direction, timing, and intensity of gene flow. Our analysis leads to a phylogeny with introgression events that differ from those obtained in previous studies. We find that Heliconius aoede most likely represents the earliest-branching lineage of the genus and that 'silvaniform' species are paraphyletic within the melpomene-silvaniform group. Our phylogeny provides new, parsimonious histories for the origins of key traits in Heliconius, including pollen feeding and an inversion involved in wing pattern mimicry. Our results demonstrate the power and feasibility of the full-likelihood MSC approach for estimating species phylogeny and key population parameters despite extensive gene flow. The methods used here should be useful for analysis of other difficult species groups with high rates of introgression.
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Affiliation(s)
| | - Fernando Seixas
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College LondonLondonUnited Kingdom
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
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6
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Bergman J, Pedersen RØ, Lundgren EJ, Lemoine RT, Monsarrat S, Pearce EA, Schierup MH, Svenning JC. Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change. Nat Commun 2023; 14:7679. [PMID: 37996436 PMCID: PMC10667484 DOI: 10.1038/s41467-023-43426-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
The worldwide extinction of megafauna during the Late Pleistocene and Early Holocene is evident from the fossil record, with dominant theories suggesting a climate, human or combined impact cause. Consequently, two disparate scenarios are possible for the surviving megafauna during this time period - they could have declined due to similar pressures, or increased in population size due to reductions in competition or other biotic pressures. We therefore infer population histories of 139 extant megafauna species using genomic data which reveal population declines in 91% of species throughout the Quaternary period, with larger species experiencing the strongest decreases. Declines become ubiquitous 32-76 kya across all landmasses, a pattern better explained by worldwide Homo sapiens expansion than by changes in climate. We estimate that, in consequence, total megafauna abundance, biomass, and energy turnover decreased by 92-95% over the past 50,000 years, implying major human-driven ecosystem restructuring at a global scale.
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Affiliation(s)
- Juraj Bergman
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark.
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark.
| | - Rasmus Ø Pedersen
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Erick J Lundgren
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Rhys T Lemoine
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Sophie Monsarrat
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Rewilding Europe, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
| | - Elena A Pearce
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Jens-Christian Svenning
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
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7
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Chen X, Wang Z, Zhang C, Hu J, Lu Y, Zhou H, Mei Y, Cong Y, Guo F, Wang Y, He K, Liu Y, Li F. Unraveling the complex evolutionary history of lepidopteran chromosomes through ancestral chromosome reconstruction and novel chromosome nomenclature. BMC Biol 2023; 21:265. [PMID: 37981687 PMCID: PMC10658929 DOI: 10.1186/s12915-023-01762-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 11/06/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Lepidoptera is one of the most species-rich animal groups, with substantial karyotype variations among species due to chromosomal rearrangements. Knowledge of the evolutionary patterns of lepidopteran chromosomes still needs to be improved. RESULTS Here, we used chromosome-level genome assemblies of 185 lepidopteran insects to reconstruct an ancestral reference genome and proposed a new chromosome nomenclature. Thus, we renamed over 5000 extant chromosomes with this system, revealing the historical events of chromosomal rearrangements and their features. Additionally, our findings indicate that, compared with autosomes, the Z chromosome in Lepidoptera underwent a fast loss of conserved genes, rapid acquisition of lineage-specific genes, and a low rate of gene duplication. Moreover, we presented evidence that all available 67 W chromosomes originated from a common ancestor chromosome, with four neo-W chromosomes identified, including one generated by fusion with an autosome and three derived through horizontal gene transfer. We also detected nearly 4000 inter-chromosomal gene movement events. Notably, Geminin is transferred from the autosome to the Z chromosome. When located on the autosome, Geminin shows female-biased expression, but on the Z chromosome, it exhibits male-biased expression. This contributes to the sexual dimorphism of body size in silkworms. CONCLUSIONS Our study sheds light on the complex evolutionary history of lepidopteran chromosomes based on ancestral chromosome reconstruction and novel chromosome nomenclature.
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Affiliation(s)
- Xi Chen
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zuoqi Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Chaowei Zhang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jingheng Hu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yueqi Lu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Hang Zhou
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yuyang Cong
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fangyuan Guo
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Ying Liu
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.
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8
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Wang Z, Luo W, Ping J, Xia Y, Ran J, Zeng X. Large X-effects are absent in torrent frogs with nascent sex chromosomes. Mol Ecol 2023; 32:5338-5349. [PMID: 37602937 DOI: 10.1111/mec.17113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/23/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023]
Abstract
Sex chromosomes are popularized as a special role in driving speciation. However, the empirical evidence from natural population processes has been limited to organisms with degenerated sex chromosomes, where hemizygosity is mainly considered to act as the driver of reproductive isolation. Here, we examined several hybrid zones of torrent frog Amolops mantzorum species complex, using an approach by mapping species-diagnostic loci onto the reference genome to compare sex-linked versus autosomal patterns of introgression. We find little support in sex-linked incompatibilities for large X-effects for these populations in hybrid zones with homomorphic sex chromosomes, due to the absence of the hemizygous effects. As expected, the large X-effects were not found in those with heteromorphic but newly evolved sex chromosomes, owing to the absence of strong genetic differences between X and Y chromosomes. The available data so far on amphibians suggest little role for sex-linked genes in speciation. The large X-effects in those with nascent sex chromosomes may not be as ubiquitous as presumed across the animal kingdom.
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Affiliation(s)
- Ziwen Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Luo
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Jun Ping
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yun Xia
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jianghong Ran
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaomao Zeng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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9
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Laetsch DR, Bisschop G, Martin SH, Aeschbacher S, Setter D, Lohse K. Demographically explicit scans for barriers to gene flow using gIMble. PLoS Genet 2023; 19:e1010999. [PMID: 37816069 PMCID: PMC10610087 DOI: 10.1371/journal.pgen.1010999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/27/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Identifying regions of the genome that act as barriers to gene flow between recently diverged taxa has remained challenging given the many evolutionary forces that generate variation in genetic diversity and divergence along the genome, and the stochastic nature of this variation. Progress has been impeded by a conceptual and methodological divide between analyses that infer the demographic history of speciation and genome scans aimed at identifying locally maladaptive alleles i.e. genomic barriers to gene flow. Here we implement genomewide IM blockwise likelihood estimation (gIMble), a composite likelihood approach for the quantification of barriers, that bridges this divide. This analytic framework captures background selection and selection against barriers in a model of isolation with migration (IM) as heterogeneity in effective population size (Ne) and effective migration rate (me), respectively. Variation in both effective demographic parameters is estimated in sliding windows via pre-computed likelihood grids. gIMble includes modules for pre-processing/filtering of genomic data and performing parametric bootstraps using coalescent simulations. To demonstrate the new approach, we analyse data from a well-studied pair of sister species of tropical butterflies with a known history of post-divergence gene flow: Heliconius melpomene and H. cydno. Our analyses uncover both large-effect barrier loci (including well-known wing-pattern genes) and a genome-wide signal of a polygenic barrier architecture.
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Affiliation(s)
- Dominik R. Laetsch
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Gertjan Bisschop
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Simon H. Martin
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Derek Setter
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Konrad Lohse
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
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10
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Hatchett WJ, Jueterbock AO, Kopp M, Coyer JA, Coelho SM, Hoarau G, Lipinska AP. Evolutionary dynamics of sex-biased gene expression in a young XY system: insights from the brown alga genus Fucus. THE NEW PHYTOLOGIST 2023; 238:422-437. [PMID: 36597732 DOI: 10.1111/nph.18710] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Sex-biased gene expression is considered to be an underlying cause of sexually dimorphic traits. Although the nature and degree of sex-biased expression have been well documented in several animal and plant systems, far less is known about the evolution of sex-biased genes in more distant eukaryotic groups. Here, we investigate sex-biased gene expression in two brown algal dioecious species, Fucus serratus and Fucus vesiculosus, where male heterogamety (XX/XY) has recently emerged. We find that in contrast to evolutionary distant plant and animal lineages, male-biased genes do not experience high turnover rates, but instead reveal remarkable conservation of bias and expression levels between the two species, suggesting their importance in sexual differentiation. Genes with consistent male bias were enriched in functions related to gamete production, along with sperm competition and include three flagellar proteins under positive selection. We present one of the first reports, outside of the animal kingdom, showing that male-biased genes display accelerated rates of coding sequence evolution compared with female-biased or unbiased genes. Our results imply that evolutionary forces affect male and female sex-biased genes differently on structural and regulatory levels, resulting in unique properties of differentially expressed transcripts during reproductive development in Fucus algae.
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Affiliation(s)
- William J Hatchett
- Faculty of Biosciences and Aquaculture, Nord University, 8026, Bodø, Norway
| | | | - Martina Kopp
- Faculty of Biosciences and Aquaculture, Nord University, 8026, Bodø, Norway
| | - James A Coyer
- Shoals Marine Laboratory, University of New Hampshire, Durham, NH, 03824, USA
| | - Susana M Coelho
- CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, Station Biologique de Roscoff, 29680, Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tuebingen, Germany
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, 8026, Bodø, Norway
| | - Agnieszka P Lipinska
- CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, Station Biologique de Roscoff, 29680, Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tuebingen, Germany
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11
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Yusuf LH, Tyukmaeva V, Hoikkala A, Ritchie MG. Divergence and introgression among the virilis group of Drosophila. Evol Lett 2022; 6:537-551. [PMID: 36579165 PMCID: PMC9783487 DOI: 10.1002/evl3.301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 09/23/2022] [Accepted: 10/12/2022] [Indexed: 12/03/2022] Open
Abstract
Speciation with gene flow is now widely regarded as common. However, the frequency of introgression between recently diverged species and the evolutionary consequences of gene flow are still poorly understood. The virilis group of Drosophila contains 12 species that are geographically widespread and show varying levels of prezygotic and postzygotic isolation. Here, we use de novo genome assemblies and whole-genome sequencing data to resolve phylogenetic relationships and describe patterns of introgression and divergence across the group. We suggest that the virilis group consists of three, rather than the traditional two, subgroups. Some genes undergoing rapid sequence divergence across the group were involved in chemical communication and desiccation tolerance, and may be related to the evolution of sexual isolation and adaptation. We found evidence of pervasive phylogenetic discordance caused by ancient introgression events between distant lineages within the group, and more recent gene flow between closely related species. When assessing patterns of genome-wide divergence in species pairs across the group, we found no consistent genomic evidence of a disproportionate role for the X chromosome as has been found in other systems. Our results show how ancient and recent introgressions confuse phylogenetic reconstruction, but may play an important role during early radiation of a group.
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Affiliation(s)
- Leeban H. Yusuf
- Centre for Biological Diversity, School of BiologyUniversity of St AndrewsSt AndrewsKY16 9THUnited Kingdom
| | - Venera Tyukmaeva
- Centre for Biological Diversity, School of BiologyUniversity of St AndrewsSt AndrewsKY16 9THUnited Kingdom
- Department of Evolution, Ecology and BehaviourUniversity of LiverpoolLiverpoolL69 7ZBUnited Kingdom
| | - Anneli Hoikkala
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskylä40014Finland
| | - Michael G. Ritchie
- Centre for Biological Diversity, School of BiologyUniversity of St AndrewsSt AndrewsKY16 9THUnited Kingdom
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12
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vonHoldt BM, Brzeski KE, Aardema ML, Schell CJ, Rutledge LY, Fain SR, Shutt AC, Linderholm A, Murphy WJ. Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast. Mol Ecol 2022; 31:5440-5454. [PMID: 34585803 DOI: 10.1111/mec.16200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/03/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022]
Abstract
Admixture and introgression play a critical role in adaptation and genetic rescue that has only recently gained a deeper appreciation. Here, we explored the geographical and genomic landscape of cryptic ancestry of the endangered red wolf that persists within the genome of a ubiquitous sister taxon, the coyote, all while the red wolf has been extinct in the wild since the early 1980s. We assessed admixture across 120,621 single nucleotiode polymorphism (SNP) loci genotyped in 293 canid genomes. We found support for increased red wolf ancestry along a west-to-east gradient across the southern United States associated with historical admixture in the past 100 years. Southwestern Louisiana and southeastern Texas, the geographical zone where the last red wolves were known prior to extinction in the wild, contained the highest and oldest levels of red wolf ancestry. Further, given the paucity of inferences based on chromosome types, we compared patterns of ancestry on the X chromosome and autosomes. We additionally aimed to explore the relationship between admixture timing and recombination rate variation to investigate gene flow events. We found that X-linked regions of low recombination rates were depleted of introgression, relative to the autosomes, consistent with the large X effect and enrichment with loci involved in maintaining reproductive isolation. Recombination rate was positively correlated with red wolf ancestry across coyote genomes, consistent with theoretical predictions. The geographical and genomic extent of cryptic red wolf ancestry can provide novel genomic resources for recovery plans targeting the conservation of the endangered red wolf.
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Affiliation(s)
- Bridgett M vonHoldt
- Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, Michigan, USA
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, New Jersey, USA.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Christopher J Schell
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
| | - Linda Y Rutledge
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Steven R Fain
- USFWS, Clark R. Bavin National Forensics Laboratory, Ashland, Oregon, USA
| | | | - Anna Linderholm
- Department of Anthropology, Texas A&M University, College Station, Texas, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
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13
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Ruggieri AA, Livraghi L, Lewis JJ, Evans E, Cicconardi F, Hebberecht L, Ortiz-Ruiz Y, Montgomery SH, Ghezzi A, Rodriguez-Martinez JA, Jiggins CD, McMillan WO, Counterman BA, Papa R, Van Belleghem SM. A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility. Genome Res 2022; 32:1862-1875. [PMID: 36109150 PMCID: PMC9712634 DOI: 10.1101/gr.276839.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 09/13/2022] [Indexed: 01/16/2023]
Abstract
Despite insertions and deletions being the most common structural variants (SVs) found across genomes, not much is known about how much these SVs vary within populations and between closely related species, nor their significance in evolution. To address these questions, we characterized the evolution of indel SVs using genome assemblies of three closely related Heliconius butterfly species. Over the relatively short evolutionary timescales investigated, up to 18.0% of the genome was composed of indels between two haplotypes of an individual Heliconius charithonia butterfly and up to 62.7% included lineage-specific SVs between the genomes of the most distant species (11 Mya). Lineage-specific sequences were mostly characterized as transposable elements (TEs) inserted at random throughout the genome and their overall distribution was similarly affected by linked selection as single nucleotide substitutions. Using chromatin accessibility profiles (i.e., ATAC-seq) of head tissue in caterpillars to identify sequences with potential cis-regulatory function, we found that out of the 31,066 identified differences in chromatin accessibility between species, 30.4% were within lineage-specific SVs and 9.4% were characterized as TE insertions. These TE insertions were localized closer to gene transcription start sites than expected at random and were enriched for sites with significant resemblance to several transcription factor binding sites with known function in neuron development in Drosophila We also identified 24 TE insertions with head-specific chromatin accessibility. Our results show high rates of structural genome evolution that were previously overlooked in comparative genomic studies and suggest a high potential for structural variation to serve as raw material for adaptive evolution.
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Affiliation(s)
- Angelo A Ruggieri
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
| | - Luca Livraghi
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Smithsonian Tropical Research Institute, Apartado 0843-03092 Panamá, Panama
| | - James J Lewis
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Elizabeth Evans
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
| | - Francesco Cicconardi
- School of Biological Sciences, Bristol University, Bristol BS8 1QU, United Kingdom
| | - Laura Hebberecht
- School of Biological Sciences, Bristol University, Bristol BS8 1QU, United Kingdom
| | - Yadira Ortiz-Ruiz
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan 00926, Puerto Rico
| | - Stephen H Montgomery
- School of Biological Sciences, Bristol University, Bristol BS8 1QU, United Kingdom
| | - Alfredo Ghezzi
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Apartado 0843-03092 Panamá, Panama
| | - Brian A Counterman
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan 00926, Puerto Rico
| | - Steven M Van Belleghem
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
- Ecology, Evolution and Conservation Biology, Biology Department, KU Leuven, 3000 Leuven, Belgium
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14
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Pereira Martins AR, Martins LP, Ho W, McMillan WO, Ready JS, Barrett R. Scale-dependent environmental effects on phenotypic distributions in Heliconius butterflies. Ecol Evol 2022; 12:e9286. [PMID: 36177141 PMCID: PMC9471044 DOI: 10.1002/ece3.9286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/08/2022] [Accepted: 08/17/2022] [Indexed: 01/26/2023] Open
Abstract
Identifying the relative importance of different mechanisms responsible for the emergence and maintenance of phenotypic diversity can be challenging, as multiple selective pressures and stochastic events are involved in these processes. Therefore, testing how environmental conditions shape the distribution of phenotypes can offer important insights on local adaptation, divergence, and speciation. The red-yellow Müllerian mimicry ring of Heliconius butterflies exhibits a wide diversity of color patterns across the Neotropics and is involved in multiple hybrid zones, making it a powerful system to investigate environmental drivers of phenotypic distributions. Using the distantly related Heliconius erato and Heliconius melpomene co-mimics and a multiscale distribution approach, we investigated whether distinct phenotypes of these species are associated with different environmental conditions. We show that Heliconius red-yellow phenotypic distribution is strongly driven by environmental gradients (especially thermal and precipitation variables), but that phenotype and environment associations vary with spatial scale. While co-mimics are usually predicted to occur in similar environments at large spatial scales, patterns at local scales are not always consistent (i.e., different variables are best predictors of phenotypic occurrence in different locations) or congruent (i.e., co-mimics show distinct associations with environment). We suggest that large-scale analyses are important for identifying how environmental factors shape broad mimetic phenotypic distributions, but that local studies are essential to understand the context-dependent biotic, abiotic, and historical mechanisms driving finer-scale phenotypic transitions.
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Affiliation(s)
- Ananda R. Pereira Martins
- Redpath MuseumMcGill UniversityMontrealQuebecCanada
- Smithsonian Tropical Research InstitutePanama CityPanama
| | - Lucas P. Martins
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | | | | | - Jonathan S. Ready
- Instituto de Ciências BiológicasUniversidade Federal do ParáBelémBrazil
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15
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Repeated genetic adaptation to altitude in two tropical butterflies. Nat Commun 2022; 13:4676. [PMID: 35945236 PMCID: PMC9363431 DOI: 10.1038/s41467-022-32316-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 07/26/2022] [Indexed: 01/02/2023] Open
Abstract
Repeated evolution can provide insight into the mechanisms that facilitate adaptation to novel or changing environments. Here we study adaptation to altitude in two tropical butterflies, Heliconius erato and H. melpomene, which have repeatedly and independently adapted to montane habitats on either side of the Andes. We sequenced 518 whole genomes from altitudinal transects and found many regions differentiated between highland (~ 1200 m) and lowland (~ 200 m) populations. We show repeated genetic differentiation across replicate populations within species, including allopatric comparisons. In contrast, there is little molecular parallelism between the two species. By sampling five close relatives, we find that a large proportion of divergent regions identified within species have arisen from standing variation and putative adaptive introgression from high-altitude specialist species. Taken together our study supports a role for both standing genetic variation and gene flow from independently adapted species in promoting parallel local adaptation to the environment. Here, the authors study adaptation to altitude in 518 whole genomes from two species of tropical butterflies. They find repeated genetic differentiation within species, little molecular parallelism between these species, and introgression from closely related species, concluding that standing genetic variation promotes parallel local adaptation.
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16
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Robbins RK, Cong Q, Zhang J, Shen J, Busby RC, Faynel C, Duarte M, Martins ARP, Prieto C, Lamas G, Grishin NV. Genomics-based higher classification of the species-rich Hairstreaks (Lepidoptera: Lycaenidae: Eumaeini). SYSTEMATIC ENTOMOLOGY 2022; 47:445-469. [PMID: 35782754 PMCID: PMC9246340 DOI: 10.1111/syen.12541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We propose a higher classification of the lycaenid hairstreak tribe Eumaeini - one of the youngest and most species-rich butterfly tribes - based on autosome, Lepidopteran Z sex chromosome, and mitochondrial protein-coding genes. The subtribe Neolycaenina Korb is a synonym of Callophryidina Tutt, and subtribe Tmolusina Bálint is a synonym of Strephonotina K. Johnson, Austin, Le Crom, & Salazar. Proposed names are Rhammina Prieto & Busby, new subtribe; Timaetina Busby & Prieto, new subtribe; Atlidina Martins & Duarte, new subtribe; Evenina Faynel & Grishin, new subtribe; Jantheclina Robbins & Faynel, new subtribe; Paiwarriina Lamas & Robbins, new subtribe; Cupatheclina Lamas & Grishin, new subtribe; Parrhasiina Busby & Robbins, new subtribe; Ipideclina Martins & Grishin, new subtribe; and Trichonidina Duarte & Faynel, new subtribe. Phylogenetic results from the autosome and Z sex chromosome analyses are similar. Future analyses of datasets with hundreds of terminal taxa may be more practical time-wise by focussing on the smaller number of sex chromosome sequences (2.6% of nuclear protein-coding sequences). The phylogenetic classification and biological summaries for each subtribe suggest that a variety of factors affected Eumaeini diversification. About a dozen kinds of male secondary sexual organs with frequent evolutionary gains and losses occur in Atlidina, Evenina, and Jantheclina (141 species combined). Females have been shown to use these organs to discriminate between conspecific and non-conspecific males, facilitating sympatry among close relatives. Eumaeina, Rhammina, and Timaetina (140 species combined) are overwhelmingly montane with some evidence for a higher incidence of sympatric diversification. Seven Neotropical lineages in five subtribes invaded the temperate parts of the Nearctic Region with a diversification increase in the Callophryidina (262 species). North American Satyrium and Callophrys then invaded the Palearctic at least once each, with a major species-richness increase in Satyrium. The evolution of litter feeding detritivores within Calycopidina (172 species) resulted in an increase in diversification rate compared with its flower-feeding sister lineage. Atlidina, Strephonotina, Parrhasiina, and Strymonina (562 species combined) each contain a mixture of genera that specialize on one or two caterpillar food plant families and genera that are polyphagous. These would be appropriate subtribes to assess how the breadth of caterpillar food plants and the frequency of host shifts affected diversification.
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Affiliation(s)
- Robert K Robbins
- Department of Entomology, National Museum of Natural History, PO Box 37012, NHB Stop 105, Smithsonian Institution, Washington, D.C., USA
| | - Qian Cong
- Department of Biochemistry, University of Washington, Seattle, WA, 98105, USA
| | - Jing Zhang
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, USA
| | - Jinhui Shen
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, USA
| | | | | | - Marcelo Duarte
- Museu de Zoologia, Universidade de São Paulo, Avenida Nazaré 481, Ipiranga, 04263-000, São Paulo, SP, Brazil
| | - Ananda R P Martins
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Canada, H3A0C4
| | - Carlos Prieto
- Departamento de Biología, Universidad del Atlántico, Barranquilla, Colombia and Corporación Universitaria Autónoma del Cauca, Popayán, Colombia
| | - Gerardo Lamas
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Apartado 14-0434, Lima-14, Peru
| | - Nick V Grishin
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9050, USA
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17
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Tigano A, Khan R, Omer AD, Weisz D, Dudchenko O, Multani AS, Pathak S, Behringer RR, Aiden EL, Fisher H, MacManes MD. Chromosome size affects sequence divergence between species through the interplay of recombination and selection. Evolution 2022; 76:782-798. [PMID: 35271737 PMCID: PMC9314927 DOI: 10.1111/evo.14467] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 12/12/2021] [Indexed: 01/21/2023]
Abstract
The structure of the genome shapes the distribution of genetic diversity and sequence divergence. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we combined empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from three different mammalian clades-Peromyscus rodents, Mus mice, and great apes-from chromosome-level genome assemblies. We found a strong significant negative correlation between chromosome size and sequence divergence in all species comparisons within the Peromyscus and great apes clades but not the Mus clade, suggesting that the dramatic chromosomal rearrangements among Mus species may have masked the ancestral genomic landscape of divergence in many comparisons. Our evolutionary simulations showed that the main factor determining differences in divergence among chromosomes of different sizes is the interplay of recombination rate and selection, with greater variation in larger populations than in smaller ones. In ancestral populations, shorter chromosomes harbor greater nucleotide diversity. As ancestral populations diverge, diversity present at the onset of the split contributes to greater sequence divergence in shorter chromosomes among daughter species. The combination of empirical data and evolutionary simulations revealed that chromosomal rearrangements, demography, and divergence times may also affect the relationship between chromosome size and divergence, thus deepening our understanding of the role of genome structure in the evolution of species divergence.
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Affiliation(s)
- Anna Tigano
- Molecular, Cellular, and Biomedical Sciences DepartmentUniversity of New HampshireDurhamNH03824USA,Hubbard Center for Genome StudiesUniversity of New HampshireDurhamNH03824USA,Current address: Department of BiologyUniversity of British Columbia – Okanagan CampusKelownaBCV1 V 1V7Canada
| | - Ruqayya Khan
- The Center for Genome ArchitectureDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Arina D. Omer
- The Center for Genome ArchitectureDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - David Weisz
- The Center for Genome ArchitectureDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Olga Dudchenko
- The Center for Genome ArchitectureDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA,Department of Computer ScienceDepartment of Computational and Applied MathematicsRice UniversityHoustonTX77030USA
| | - Asha S. Multani
- Department of GeneticsM.D. Anderson Cancer CenterUniversity of TexasHoustonTX77030USA
| | - Sen Pathak
- Department of GeneticsM.D. Anderson Cancer CenterUniversity of TexasHoustonTX77030USA
| | - Richard R. Behringer
- Department of GeneticsM.D. Anderson Cancer CenterUniversity of TexasHoustonTX77030USA
| | - Erez L. Aiden
- The Center for Genome ArchitectureDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA,Department of Computer ScienceDepartment of Computational and Applied MathematicsRice UniversityHoustonTX77030USA,Center for Theoretical and Biological PhysicsRice UniversityHoustonTX77030USA,Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China,School of Agriculture and EnvironmentUniversity of Western AustraliaPerthWA6009Australia
| | - Heidi Fisher
- Department of BiologyUniversity of MarylandCollege ParkMD20742USA
| | - Matthew D. MacManes
- Molecular, Cellular, and Biomedical Sciences DepartmentUniversity of New HampshireDurhamNH03824USA,Hubbard Center for Genome StudiesUniversity of New HampshireDurhamNH03824USA
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18
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Zhang J, Zhang F, Tay WT, Robin C, Shi Y, Guan F, Yang Y, Wu Y. Population genomics provides insights into lineage divergence and local adaptation within the cotton bollworm. Mol Ecol Resour 2022; 22:1875-1891. [PMID: 35007400 DOI: 10.1111/1755-0998.13581] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/20/2021] [Accepted: 01/05/2022] [Indexed: 11/28/2022]
Abstract
The cotton bollworm Helicoverpa armigera is a cosmopolitan pest and its diverse habitats plausibly contribute to the formation of diverse lineages. Despite the significant threat it poses to economic crops worldwide, its evolutionary history and genetic basis of local adaptation are poorly understood. In this study, we de novo assembled a high-quality chromosome-level reference genome of H. a. armigera (contig N50 = 7.34 Mb), with 99.13% of the HaSCD2 assembly assigned into 31 chromosomes (Z-chromosome + 30 autosomes). We constructed an ultra-dense variation map across 14 cotton bollworm populations and identified a novel lineage in northwestern China. Historical inference showed that effective population size changes coincided with global temperature fluctuation. We identified nine differentiated genes in the three H. armigera lineages (H. a. armigera, H. a. conferta, and the new northwestern Chinese lineage), of which per and clk genes are involved in circadian rhythm. Selective sweep analyses identified a series of GO categories related to climate adaptation, feeding behavior and insecticide tolerance. Our findings reveal fundamental knowledge of the local adaptation of different cotton bollworm lineages and will guide the formulation of cotton bollworm management measures at different scales.
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Affiliation(s)
- Jianpeng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wee Tek Tay
- CSIRO Black Mountain Laboratories, Clunies Ross Street, ACT, 2601, Australia
| | - Charles Robin
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yu Shi
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fang Guan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yihua Yang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yidong Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
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19
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Nelson ED, Cong Q, Grishin NV. Influence of the large-Z effect during contact between butterfly sister species. Ecol Evol 2021; 11:11615-11626. [PMID: 34522328 PMCID: PMC8427592 DOI: 10.1002/ece3.7785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 11/14/2022] Open
Abstract
Recently diverged butterfly populations in North America have been found to exhibit high levels of divergence on the Z chromosome relative to autosomes, as measured by fixation index, F st . The pattern of divergence appears to result from accumulation of incompatible alleles, obstructing introgression on the Z chromosome in hybrids (i.e., the large-Z effect); however, it is unknown whether this mechanism is sufficient to explain the data. Here, we simulate the effects of hybrid incompatibility on interbreeding butterfly populations using a model in which populations accumulate cross-incompatible alleles in allopatry prior to contact. We compute statistics for introgression and population divergence during contact between model populations and compare our results to those for 15 pairs of butterfly species interbreeding along a suture zone in central Texas. Time scales for allopatry and contact in the model are scaled to glacial and interglacial periods during which real populations evolved in isolation and contact. We find that the data for butterflies are explained well by an otherwise neutral model under slow fusion conditions. In particular, levels of divergence on the Z chromosome increase when interacting clusters of genes are closely linked, consistent with clusters of functionally related genes in butterfly genomes.
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Affiliation(s)
- Erik D. Nelson
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Qian Cong
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Nick V. Grishin
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA
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20
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Liu X, Ogilvie HA, Nakhleh L. Variational inference using approximate likelihood under the coalescent with recombination. Genome Res 2021; 31:2107-2119. [PMID: 34426513 PMCID: PMC8559707 DOI: 10.1101/gr.273631.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 08/17/2021] [Indexed: 11/30/2022]
Abstract
Coalescent methods are proven and powerful tools for population genetics, phylogenetics, epidemiology, and other fields. A promising avenue for the analysis of large genomic alignments, which are increasingly common, is coalescent hidden Markov model (coalHMM) methods, but these methods have lacked general usability and flexibility. We introduce a novel method for automatically learning a coalHMM and inferring the posterior distributions of evolutionary parameters using black-box variational inference, with the transition rates between local genealogies derived empirically by simulation. This derivation enables our method to work directly with three or four taxa and through a divide-and-conquer approach with more taxa. Using a simulated data set resembling a human–chimp–gorilla scenario, we show that our method has comparable or better accuracy to previous coalHMM methods. Both species divergence times and population sizes were accurately inferred. The method also infers local genealogies, and we report on their accuracy. Furthermore, we discuss a potential direction for scaling the method to larger data sets through a divide-and-conquer approach. This accuracy means our method is useful now, and by deriving transition rates by simulation, it is flexible enough to enable future implementations of various population models.
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Affiliation(s)
- Xinhao Liu
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Huw A Ogilvie
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Luay Nakhleh
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
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21
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Van Belleghem SM, Lewis JJ, Rivera ES, Papa R. Heliconius butterflies: a window into the evolution and development of diversity. Curr Opin Genet Dev 2021; 69:72-81. [PMID: 33714874 PMCID: PMC8364860 DOI: 10.1016/j.gde.2021.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 10/21/2022]
Abstract
Butterflies have become prominent models for studying the evolution and development of phenotypic variation. In Heliconius, extraordinary within species divergence and between species convergence in wing color patterns has driven decades of comparative genetic studies. However, connecting genetic patterns of diversification to the molecular mechanisms of adaptation has remained elusive. Recent studies are bridging this gap between genome and function and have driven substantial advances in deciphering the genetic architecture of diversification in Heliconius. While only a handful of large-effect genes were initially identified in the diversification of Heliconius color patterns, recent experiments have begun to unravel the underlying gene regulatory networks and how these have evolved. These results reveal an evolutionary story of many interacting loci and partly independent genetic architectures that underlie convergent evolution.
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Affiliation(s)
| | - James J Lewis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA; Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Edgardo S Rivera
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan, Puerto Rico; Chairs of Biomaterials, University of Bayreuth, Bayreuth, Bayern, Germany
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan, Puerto Rico; Molecular Sciences and Research Center, University of Puerto Rico, San Juan, Puerto Rico.
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22
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Pazhenkova EA, Lukhtanov VA. Genomic introgression from a distant congener in the Levant fritillary butterfly, Melitaea acentria. Mol Ecol 2021; 30:4819-4832. [PMID: 34288183 DOI: 10.1111/mec.16085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
Abstract
Introgressive hybridization is more common in nature than previously thought, and its role and creative power in evolution is hotly discussed but not completely understood. Introgression occurs more frequently in sympatry between recently diverged taxa, or when the speciation process has not yet been completed. However, there are relatively few documented cases of hybridization that erodes reproductive barriers between distantly related species. Here, we use whole genome and mitochondrial data to examine how introgression from a distant congener affects pattern of genetic differentiation in the Levant fritillary butterfly Melitaea acentria. We show that this local taxon has evolved as a peripatric geographic isolate of the widespread Melitaea persea, and that there has been significant unidirectional gene flow from the sympatric, nonclosely related Melitaea didyma to M. acentria. We found direct evidence of ongoing sporadic hybridization between M. didyma and M. acentria, which are separated by at least 5 million years of independent evolution. Elevated differentiation and lower level of introgression on the sex Z chromosome compared to autosomes suggest that the Z chromosome has accumulated loci acting as intrinsic postzygotic barriers. Our results show that introgression from M. didyma has been an additional source of nucleotide diversity in the M. acentria population, providing material for drift and selection.
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Affiliation(s)
- Elena A Pazhenkova
- Department of Entomology, St. Petersburg State University, St. Petersburg, Russia.,Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
| | - Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
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23
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Comeault AA, Kautt AF, Matute DR. Genomic signatures of admixture and selection are shared among populations of Zaprionus indianus across the western hemisphere. Mol Ecol 2021; 30:6193-6210. [PMID: 34233050 PMCID: PMC9290797 DOI: 10.1111/mec.16066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/27/2021] [Accepted: 07/01/2021] [Indexed: 11/28/2022]
Abstract
Introduced species have become an increasingly common component of biological communities around the world. A central goal in invasion biology is therefore to identify the demographic and evolutionary factors that underlie successful introductions. Here we use whole genome sequences, collected from populations in the native and introduced range of the African fig fly, Zaprionus indianus, to quantify genetic relationships among them, identify potential sources of the introductions, and test for selection at different spatial scales. We find that geographically widespread populations in the western hemisphere are genetically more similar to each other than to lineages sampled across Africa, and that these populations share a mixture of alleles derived from differentiated African lineages. Using patterns of allele‐sharing and demographic modelling we show that Z. indinaus have undergone a single expansion across the western hemisphere with admixture between African lineages predating this expansion. We also find support for selection that is shared across populations in the western hemisphere, and in some cases, with a subset of African populations. This suggests either that parallel selection has acted across a large part of Z. indianus's introduced range; or, more parsimoniously, that Z. indianus has experienced selection early on during (or prior‐to) its expansion into the western hemisphere. We suggest that the range expansion of Z. indianus has been facilitated by admixture and selection, and that management of this invasion could focus on minimizing future admixture by controlling the movement of individuals within this region rather than between the western and eastern hemisphere.
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Affiliation(s)
- Aaron A Comeault
- Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, Bangor, UK
| | - Andreas F Kautt
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Daniel R Matute
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
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24
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Lewis JJ, Cicconardi F, Martin SH, Reed RD, Danko CG, Montgomery SH. The Dryas iulia Genome Supports Multiple Gains of a W Chromosome from a B Chromosome in Butterflies. Genome Biol Evol 2021; 13:evab128. [PMID: 34117762 PMCID: PMC8290107 DOI: 10.1093/gbe/evab128] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2021] [Indexed: 12/17/2022] Open
Abstract
In butterflies and moths, which exhibit highly variable sex determination mechanisms, the homogametic Z chromosome is deeply conserved and is featured in many genome assemblies. The evolution and origin of the female W sex chromosome, however, remains mostly unknown. Previous studies have proposed that a ZZ/Z0 sex determination system is ancestral to Lepidoptera, and that W chromosomes may originate from sex-linked B chromosomes. Here, we sequence and assemble the female Dryas iulia genome into 32 highly contiguous ordered and oriented chromosomes, including the Z and W sex chromosomes. We then use sex-specific Hi-C, ATAC-seq, PRO-seq, and whole-genome DNA sequence data sets to test if features of the D. iulia W chromosome are consistent with a hypothesized B chromosome origin. We show that the putative W chromosome displays female-associated DNA sequence, gene expression, and chromatin accessibility to confirm the sex-linked function of the W sequence. In contrast with expectations from studies of homologous sex chromosomes, highly repetitive DNA content on the W chromosome, the sole presence of domesticated repetitive elements in functional DNA, and lack of sequence homology with the Z chromosome or autosomes is most consistent with a B chromosome origin for the W, although it remains challenging to rule out extensive sequence divergence. Synteny analysis of the D. iulia W chromosome with other female lepidopteran genome assemblies shows no homology between W chromosomes and suggests multiple, independent origins of the W chromosome from a B chromosome likely occurred in butterflies.
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Affiliation(s)
- James J Lewis
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Francesco Cicconardi
- School of Biological Sciences, University of Bristol, United Kingdom
- Department of Zoology, University of Cambridge, United Kingdom
| | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, USA
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25
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Sedano-Cruz RE, Calero-Mejía H. CARACTERIZACIÓN GENÉTICA DE LA POBLACIÓN DE Heliconius sara (Nymphalidae) EN LA ISLA GORGONA, COLOMBIA. ACTA BIOLÓGICA COLOMBIANA 2021. [DOI: 10.15446/abc.v26n3.86205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
La estructura genética de poblaciones de mariposas con distribución en islas y sus pares continentales ha sido poco documentada para el neotrópico. Este estudio presenta la caracterización de una población de Heliconius sara con distribución en la Isla Gorgona, ubicada en la región del Pacífico Oriental Colombiano. Para esto se examinaron secuencias parciales de un marcador mitocondrial incluyendo información obtenida del GenBank. Se comparó la diversidad y estructura genética con sus conespecíficos continentales y también con congéneres, con los que comparte un ancestro común cercano en el clado Sapho-Sara. Para el análisis de diversidad y estructura genética se realizó un análisis molecular de varianza. Este análisis muestra que la distancia entre la población de la isla y sus pares en el continente es consistente con la variación intraespecífica observada en otras especies del género Heliconius. Para la reconstrucción de la genealogía y datación reciente en el Pleistoceno superior del grupo monofilético de secuencias de H. sara, se realizó un análisis de inferencia bayesiana, así como una de máxima verosimilitud. Del análisis demográfico se seleccionó un modelo histórico de flujo asimétrico desde la isla hacia el continente que sugiere baja resistencia de la discontinuidad geográfica a la dispersión de esta mariposa diurna desde la isla. Este es el primer estudio en examinar un posible evento de aislamiento de una población insular de mariposas en Colombia.
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26
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Van Belleghem SM, Cole JM, Montejo-Kovacevich G, Bacquet CN, McMillan WO, Papa R, Counterman BA. Selection and isolation define a heterogeneous divergence landscape between hybridizing Heliconius butterflies. Evolution 2021; 75:2251-2268. [PMID: 34019308 DOI: 10.1111/evo.14272] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 04/26/2021] [Accepted: 05/12/2021] [Indexed: 11/30/2022]
Abstract
Hybridizing species provide a powerful system to identify the processes that shape genomic variation and maintain species boundaries. However, complex histories of isolation, gene flow, and selection often generate heterogeneous genomic landscapes of divergence that complicate reconstruction of the speciation history. Here, we explore patterns of divergence to reconstruct recent speciation in the erato clade of Heliconius butterflies. We focus on the genomic landscape of divergence across three contact zones of the species H. erato and H. himera. We show that these hybridizing species have an intermediate level of divergence in the erato clade, which fits with their incomplete levels of reproductive isolation. Using demographic modeling and the relationship between admixture and divergence with recombination rate variation, we reconstruct histories of gene flow, selection, and demographic change that explain the observed patterns of genomic divergence. We find that periods of isolation and selection within populations, followed by secondary contact with asymmetrical gene flow are key factors in shaping the heterogeneous genomic landscapes. Collectively, these results highlight the effectiveness of demographic modeling and recombination rate estimates to disentangling the distinct contributions of gene flow and selection to patterns of genomic divergence.
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Affiliation(s)
| | - Jared M Cole
- Department of Biological Sciences, Mississippi State University, Mississippi State, USA.,Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | | | | | | | - Riccardo Papa
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico.,Molecular Sciences and Research Center, University of Puerto Rico, San Juan, PR
| | - Brian A Counterman
- Department of Biological Sciences, Mississippi State University, Mississippi State, USA.,Department of Biological Sciences, Auburn University, Alabama, USA
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27
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Garcia-Erill G, Kjaer MM, Albrechtsen A, Siegismund HR, Heller R. Vicariance followed by secondary gene flow in a young gazelle species complex. Mol Ecol 2020; 30:528-544. [PMID: 33226701 PMCID: PMC7898927 DOI: 10.1111/mec.15738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 01/03/2023]
Abstract
Grant's gazelles have recently been proposed to be a species complex comprising three highly divergent mtDNA lineages (Nanger granti, N. notata and N. petersii). The three lineages have nonoverlapping distributions in East Africa, but without any obvious geographical divisions, making them an interesting model for studying the early‐stage evolutionary dynamics of allopatric speciation in detail. Here, we use genomic data obtained by restriction site‐associated (RAD) sequencing of 106 gazelle individuals to shed light on the evolutionary processes underlying Grant's gazelle divergence, to characterize their genetic structure and to assess the presence of gene flow between the main lineages in the species complex. We date the species divergence to 134,000 years ago, which is recent in evolutionary terms. We find population subdivision within N. granti, which coincides with the previously suggested two subspecies, N. g. granti and N. g. robertsii. Moreover, these two lineages seem to have hybridized in Masai Mara. Perhaps more surprisingly given their extreme genetic differentiation, N. granti and N. petersii also show signs of prolonged admixture in Mkomazi, which we identified as a hybrid population most likely founded by allopatric lineages coming into secondary contact. Despite the admixed composition of this population, elevated X chromosomal differentiation suggests that selection may be shaping the outcome of hybridization in this population. Our results therefore provide detailed insights into the processes of allopatric speciation and secondary contact in a recently radiated species complex.
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Affiliation(s)
- Genís Garcia-Erill
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Michael Munkholm Kjaer
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark.,Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anders Albrechtsen
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Hans Redlef Siegismund
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Rasmus Heller
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
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28
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Lewis JJ, Van Belleghem SM, Papa R, Danko CG, Reed RD. Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone. SCIENCE ADVANCES 2020; 6:6/39/eabb8617. [PMID: 32978147 PMCID: PMC7518860 DOI: 10.1126/sciadv.abb8617] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/11/2020] [Indexed: 05/02/2023]
Abstract
Characterizing the genetic complexity of adaptation and trait evolution is a major emphasis of evolutionary biology and genetics. Incongruent findings from genetic studies have resulted in conceptual models ranging from a few large-effect loci to massively polygenic architectures. Here, we combine chromatin immunoprecipitation sequencing, Hi-C, RNA sequencing, and 40 whole-genome sequences from Heliconius butterflies to show that red color pattern diversification occurred via many genomic loci. We find that the red wing pattern master regulatory transcription factor Optix binds dozens of loci also under selection, which frequently form three-dimensional adaptive hubs with selection acting on multiple physically interacting genes. Many Optix-bound genes under selection are tied to pigmentation and wing development, and these loci collectively maintain separation between adaptive red color pattern phenotypes in natural populations. We propose a model of trait evolution where functional connections between loci may resolve much of the disparity between large-effect and polygenic evolutionary models.
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Affiliation(s)
- James J Lewis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | | | - Riccardo Papa
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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29
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Massardo D, VanKuren NW, Nallu S, Ramos RR, Ribeiro PG, Silva-Brandão KL, Brandão MM, Lion MB, Freitas AVL, Cardoso MZ, Kronforst MR. The roles of hybridization and habitat fragmentation in the evolution of Brazil's enigmatic longwing butterflies, Heliconius nattereri and H. hermathena. BMC Biol 2020; 18:84. [PMID: 32620168 PMCID: PMC7334841 DOI: 10.1186/s12915-020-00797-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/19/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Heliconius butterflies are widely distributed across the Neotropics and have evolved a stunning array of wing color patterns that mediate Müllerian mimicry and mating behavior. Their rapid radiation has been strongly influenced by hybridization, which has created new species and allowed sharing of color patterning alleles between mimetic species pairs. While these processes have frequently been observed in widespread species with contiguous distributions, many Heliconius species inhabit patchy or rare habitats that may strongly influence the origin and spread of species and color patterns. Here, we assess the effects of historical population fragmentation and unique biology on the origins, genetic health, and color pattern evolution of two rare and sparsely distributed Brazilian butterflies, Heliconius hermathena and Heliconius nattereri. RESULTS We assembled genomes and re-sequenced whole genomes of eight H. nattereri and 71 H. hermathena individuals. These species harbor little genetic diversity, skewed site frequency spectra, and high deleterious mutation loads consistent with recent population bottlenecks. Heliconius hermathena consists of discrete, strongly isolated populations that likely arose from a single population that dispersed after the last glacial maximum. Despite having a unique color pattern combination that suggested a hybrid origin, we found no genome-wide evidence that H. hermathena is a hybrid species. However, H. hermathena mimicry evolved via introgression, from co-mimetic Heliconius erato, of a small genomic region upstream of the color patterning gene cortex. CONCLUSIONS Heliconius hermathena and H. nattereri population fragmentation, potentially driven by historical climate change and recent deforestation, has significantly reduced the genetic health of these rare species. Our results contribute to a growing body of evidence that introgression of color patterning alleles between co-mimetic species appears to be a general feature of Heliconius evolution.
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Affiliation(s)
- Darli Massardo
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA
| | - Nicholas W VanKuren
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA.
| | - Sumitha Nallu
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA
| | - Renato R Ramos
- Departamento de Biologia Animal e Museu de Zoologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Pedro G Ribeiro
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Karina L Silva-Brandão
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Marcelo M Brandão
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marília B Lion
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - André V L Freitas
- Departamento de Biologia Animal e Museu de Zoologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Márcio Z Cardoso
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Marcus R Kronforst
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA.
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30
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Twomey E, Kain M, Claeys M, Summers K, Castroviejo-Fisher S, Van Bocxlaer I. Mechanisms for Color Convergence in a Mimetic Radiation of Poison Frogs. Am Nat 2020; 195:E132-E149. [PMID: 32364784 DOI: 10.1086/708157] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In animals, bright colors often evolve to mimic other species when a resemblance is selectively favored. Understanding the proximate mechanisms underlying such color mimicry can give insights into how mimicry evolves-for example, whether color convergence evolves from a shared set of mechanisms or through the evolution of novel color production mechanisms. We studied color production mechanisms in poison frogs (Dendrobatidae), focusing on the mimicry complex of Ranitomeya imitator. Using reflectance spectrometry, skin pigment analysis, electron microscopy, and color modeling, we found that the bright colors of these frogs, both within and outside the mimicry complex, are largely structural and produced by iridophores but that color production depends crucially on interactions with pigments. Color variation and mimicry are regulated predominantly by iridophore platelet thickness and, to a lesser extent, concentration of the red pteridine pigment drosopterin. Compared with each of the four morphs of model species that it resembles, R. imitator displays greater variation in both structural and pigmentary mechanisms, which may have facilitated phenotypic divergence in this species. Analyses of nonmimetic dendrobatids in other genera demonstrate that these mechanisms are widespread within the family and that poison frogs share a complex physiological "color palette" that can produce diverse and highly reflective colors.
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31
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Bourgeois YXC, Bertrand JAM, Delahaie B, Holota H, Thébaud C, Milá B. Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage. Mol Ecol 2020; 29:1137-1153. [PMID: 32107807 DOI: 10.1111/mec.15396] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 02/12/2020] [Accepted: 02/20/2020] [Indexed: 12/16/2022]
Abstract
Recently diverged taxa showing marked phenotypic and ecological diversity provide optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white-eye (Zosterops borbonicus) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographical forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associated with environmental variables. Analyses of genomic variation based on single nucleotide polymorphism data from genotyping-by-sequencing and pooled RAD-seq approaches show that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. We identified TYRP1, a Z-linked colour gene, as a likely candidate locus underlying colour variation among lowland forms. Tests of demographic models revealed that highland and lowland forms diverged in the presence of gene flow, and divergence has progressed as gene flow was restricted by selection at loci across the genome. This system holds promise for investigating how adaptation and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.
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Affiliation(s)
- Yann X C Bourgeois
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK.,Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Joris A M Bertrand
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France.,Laboratoire Génome & Développement des Plantes, UMR 5096, Université de Perpignan Via Domitia, Perpignan, France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France.,Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Hélène Holota
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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32
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Gauthier J, de Silva DL, Gompert Z, Whibley A, Houssin C, Le Poul Y, McClure M, Lemaitre C, Legeai F, Mallet J, Elias M. Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone. Mol Ecol 2020; 29:1328-1343. [PMID: 32145112 DOI: 10.1111/mec.15403] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/03/2020] [Accepted: 02/21/2020] [Indexed: 11/28/2022]
Abstract
Hybrid zones, whereby divergent lineages come into contact and eventually hybridize, can provide insights on the mechanisms involved in population differentiation and reproductive isolation, and ultimately speciation. Suture zones offer the opportunity to compare these processes across multiple species. In this paper we use reduced-complexity genomic data to compare the genetic and phenotypic structure and hybridization patterns of two mimetic butterfly species, Ithomia salapia and Oleria onega (Nymphalidae: Ithomiini), each consisting of a pair of lineages differentiated for their wing colour pattern and that come into contact in the Andean foothills of Peru. Despite similarities in their life history, we highlight major differences, both at the genomic and phenotypic level, between the two species. These differences include the presence of hybrids, variations in wing phenotype, and genomic patterns of introgression and differentiation. In I. salapia, the two lineages appear to hybridize only rarely, whereas in O. onega the hybrids are not only more common, but also genetically and phenotypically more variable. We also detected loci statistically associated with wing colour pattern variation, but in both species these loci were not over-represented among the candidate barrier loci, suggesting that traits other than wing colour pattern may be important for reproductive isolation. Our results contrast with the genomic patterns observed between hybridizing lineages in the mimetic Heliconius butterflies, and call for a broader investigation into the genomics of speciation in Ithomiini - the largest radiation of mimetic butterflies.
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Affiliation(s)
- Jérémy Gauthier
- Inria, CNRS, IRISA, University Rennes, Rennes, France.,Geneva Natural History Museum, Geneva, Switzerland
| | - Donna Lisa de Silva
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | | | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Céline Houssin
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | - Yann Le Poul
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France.,Fakultat für Biologie, Biozentrum, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Melanie McClure
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | | | | | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Marianne Elias
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
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33
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Moest M, Van Belleghem SM, James JE, Salazar C, Martin SH, Barker SL, Moreira GRP, Mérot C, Joron M, Nadeau NJ, Steiner FM, Jiggins CD. Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation. PLoS Biol 2020; 18:e3000597. [PMID: 32027643 PMCID: PMC7029882 DOI: 10.1371/journal.pbio.3000597] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 02/19/2020] [Accepted: 01/15/2020] [Indexed: 11/21/2022] Open
Abstract
Natural selection leaves distinct signatures in the genome that can reveal the targets and history of adaptive evolution. By analysing high-coverage genome sequence data from 4 major colour pattern loci sampled from nearly 600 individuals in 53 populations, we show pervasive selection on wing patterns in the Heliconius adaptive radiation. The strongest signatures correspond to loci with the greatest phenotypic effects, consistent with visual selection by predators, and are found in colour patterns with geographically restricted distributions. These recent sweeps are similar between co-mimics and indicate colour pattern turn-over events despite strong stabilising selection. Using simulations, we compare sweep signatures expected under classic hard sweeps with those resulting from adaptive introgression, an important aspect of mimicry evolution in Heliconius butterflies. Simulated recipient populations show a distinct 'volcano' pattern with peaks of increased genetic diversity around the selected target, characteristic of sweeps of introgressed variation and consistent with diversity patterns found in some populations. Our genomic data reveal a surprisingly dynamic history of colour pattern selection and co-evolution in this adaptive radiation.
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Affiliation(s)
- Markus Moest
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Steven M. Van Belleghem
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Jennifer E. James
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogota D.C., Colombia
| | - Simon H. Martin
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah L. Barker
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Gilson R. P. Moreira
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Claire Mérot
- IBIS, Department of Biology, Université Laval, Québec, Canada
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS—Université de Montpellier—Université Paul Valéry Montpellier—EPHE, Montpellier, France
| | - Nicola J. Nadeau
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | | | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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34
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Battey CJ. Evidence of linked selection on the Z chromosome of hybridizing hummingbirds. Evolution 2020; 74:725-739. [PMID: 31859363 DOI: 10.1111/evo.13888] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/01/2019] [Accepted: 11/12/2019] [Indexed: 12/25/2022]
Abstract
Levels of genetic differentiation vary widely along the genomes of recently diverged species. What processes cause this variation? Here, I analyze geographic population structure and genome-wide patterns of variation in the Rufous, Allen's, and Calliope Hummingbirds (Selasphorus rufus/Selasphorus sasin/Selasphorus calliope) and assess evidence that linked selection on the Z chromosome drives patterns of genetic differentiation in a pair of hybridizing species. Demographic models, introgression tests, and genotype clustering analyses support a reticulate evolutionary history consistent with divergence during the late Pleistocene followed by gene flow across migrant Rufous and Allen's Hummingbirds during the Holocene. Relative genetic differentiation ( F s t ) is elevated, and within-population diversity (π) is depressed on the Z chromosome in all interspecific comparisons. The ratio of Z to autosomal within-population diversity is much lower than that expected from population size effects alone, and Tajima's D is depressed on the Z chromosome in S. rufus and S. calliope. These results suggest that conserved structural features of the genome play a prominent role in shaping genetic differentiation through the early stages of speciation in northern Selasphorus hummingbirds, and that the Z chromosome is a likely site of genes underlying behavioral and morphological variation in the group.
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Affiliation(s)
- Christopher J Battey
- Department of Biology, University of Washington, Seattle, Washington, 97403-1201.,Current Address: Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403
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35
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Matute DR, Comeault AA, Earley E, Serrato-Capuchina A, Peede D, Monroy-Eklund A, Huang W, Jones CD, Mackay TFC, Coyne JA. Rapid and Predictable Evolution of Admixed Populations Between Two Drosophila Species Pairs. Genetics 2020; 214:211-230. [PMID: 31767631 PMCID: PMC6944414 DOI: 10.1534/genetics.119.302685] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/18/2019] [Indexed: 12/30/2022] Open
Abstract
The consequences of hybridization are varied, ranging from the origin of new lineages, introgression of some genes between species, to the extinction of one of the hybridizing species. We generated replicate admixed populations between two pairs of sister species of Drosophila: D. simulans and D. mauritiana; and D. yakuba and D. santomea Each pair consisted of a continental species and an island endemic. The admixed populations were maintained by random mating in discrete generations for over 20 generations. We assessed morphological, behavioral, and fitness-related traits from each replicate population periodically, and sequenced genomic DNA from the populations at generation 20. For both pairs of species, species-specific traits and their genomes regressed to those of the continental species. A few alleles from the island species persisted, but they tended to be proportionally rare among all sites in the genome and were rarely fixed within the populations. This paucity of alleles from the island species was particularly pronounced on the X-chromosome. These results indicate that nearly all foreign genes were quickly eliminated after hybridization and that selection against the minor species genome might be similar across experimental replicates.
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Affiliation(s)
- Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Aaron A Comeault
- School of Natural Sciences, Bangor University, Wales, UK LL57 2EN
| | - Eric Earley
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | | | - David Peede
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Anaïs Monroy-Eklund
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Wen Huang
- Program in Genetics and Department of Biological Science, North Carolina State University, Raleigh, North Carolina 27695
| | - Corbin D Jones
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Trudy F C Mackay
- Program in Genetics and Department of Biological Science, North Carolina State University, Raleigh, North Carolina 27695
| | - Jerry A Coyne
- Ecology and Evolution, University of Chicago, Illinois 60637
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36
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Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry. Proc Natl Acad Sci U S A 2019; 116:24174-24183. [PMID: 31712408 DOI: 10.1073/pnas.1907068116] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Color pattern mimicry in Heliconius butterflies is a classic case study of complex trait adaptation via selection on a few large effect genes. Association studies have linked color pattern variation to a handful of noncoding regions, yet the presumptive cis-regulatory elements (CREs) that control color patterning remain unknown. Here we combine chromatin assays, DNA sequence associations, and genome editing to functionally characterize 5 cis-regulatory elements of the color pattern gene optix We were surprised to find that the cis-regulatory architecture of optix is characterized by pleiotropy and regulatory fragility, where deletion of individual cis-regulatory elements has broad effects on both color pattern and wing vein development. Remarkably, we found orthologous cis-regulatory elements associate with wing pattern convergence of distantly related comimics, suggesting that parallel coevolution of ancestral elements facilitated pattern mimicry. Our results support a model of color pattern evolution in Heliconius where changes to ancient, multifunctional cis-regulatory elements underlie adaptive radiation.
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37
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Edelman NB, Frandsen PB, Miyagi M, Clavijo B, Davey J, Dikow RB, García-Accinelli G, Van Belleghem SM, Patterson N, Neafsey DE, Challis R, Kumar S, Moreira GRP, Salazar C, Chouteau M, Counterman BA, Papa R, Blaxter M, Reed RD, Dasmahapatra KK, Kronforst M, Joron M, Jiggins CD, McMillan WO, Di Palma F, Blumberg AJ, Wakeley J, Jaffe D, Mallet J. Genomic architecture and introgression shape a butterfly radiation. Science 2019; 366:594-599. [PMID: 31672890 PMCID: PMC7197882 DOI: 10.1126/science.aaw2090] [Citation(s) in RCA: 266] [Impact Index Per Article: 53.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 09/16/2019] [Indexed: 12/26/2022]
Abstract
We used 20 de novo genome assemblies to probe the speciation history and architecture of gene flow in rapidly radiating Heliconius butterflies. Our tests to distinguish incomplete lineage sorting from introgression indicate that gene flow has obscured several ancient phylogenetic relationships in this group over large swathes of the genome. Introgressed loci are underrepresented in low-recombination and gene-rich regions, consistent with the purging of foreign alleles more tightly linked to incompatibility loci. Here, we identify a hitherto unknown inversion that traps a color pattern switch locus. We infer that this inversion was transferred between lineages by introgression and is convergent with a similar rearrangement in another part of the genus. These multiple de novo genome sequences enable improved understanding of the importance of introgression and selective processes in adaptive radiation.
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Affiliation(s)
- Nathaniel B Edelman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560, USA
| | - Miriam Miyagi
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - John Davey
- Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, UK
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560, USA
| | | | - Steven M Van Belleghem
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, PR 00931-3360, Puerto Rico
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
| | - Daniel E Neafsey
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Richard Challis
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sujai Kumar
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Gilson R P Moreira
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970 Brasil
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Carrera 24, No. 63C-69, Bogotá D.C. 111221, Colombia
| | - Mathieu Chouteau
- Laboratoire Ecologie, Evolution, Interactions des Systèmes Amazoniens (LEEISA), USR 3456, Université De Guyane, CNRS Guyane, 275 Route de Montabo, 97334 Cayenne, French Guiana
| | - Brian A Counterman
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, PR 00931-3360, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, PR 00931-3360, Puerto Rico
| | - Mark Blaxter
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Kanchon K Dasmahapatra
- Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, UK
| | - Marcus Kronforst
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Mathieu Joron
- CEFE, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, EPHE, IRD, 34090 Montpellier, France
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Apartado 0843-03092 Panamá, Panama
| | | | - Andrew J Blumberg
- Department of Mathematics, University of Texas, Austin, TX 78712, USA
| | - John Wakeley
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - David Jaffe
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- 10x Genomics, Pleasanton, CA 94566, USA
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
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38
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V. Barroso G, Puzović N, Dutheil JY. Inference of recombination maps from a single pair of genomes and its application to ancient samples. PLoS Genet 2019; 15:e1008449. [PMID: 31725722 PMCID: PMC6879166 DOI: 10.1371/journal.pgen.1008449] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 11/26/2019] [Accepted: 09/30/2019] [Indexed: 12/11/2022] Open
Abstract
Understanding the causes and consequences of recombination landscape evolution is a fundamental goal in genetics that requires recombination maps from across the tree of life. Such maps can be obtained from population genomic datasets, but require large sample sizes. Alternative methods are therefore necessary to research organisms where such datasets cannot be generated easily, such as non-model or ancient species. Here we extend the sequentially Markovian coalescent model to jointly infer demography and the spatial variation in recombination rate. Using extensive simulations and sequence data from humans, fruit-flies and a fungal pathogen, we demonstrate that iSMC accurately infers recombination maps under a wide range of scenarios-remarkably, even from a single pair of unphased genomes. We exploit this possibility and reconstruct the recombination maps of ancient hominins. We report that the ancient and modern maps are correlated in a manner that reflects the established phylogeny of Neanderthals, Denisovans, and modern human populations.
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Affiliation(s)
- Gustavo V. Barroso
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, August-Thienemann-Straße , Plön–GERMANY
| | - Nataša Puzović
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, August-Thienemann-Straße , Plön–GERMANY
| | - Julien Y. Dutheil
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, August-Thienemann-Straße , Plön–GERMANY
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39
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Lavretsky P, DaCosta JM, Sorenson MD, McCracken KG, Peters JL. ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America. Mol Ecol 2019; 28:2594-2609. [DOI: 10.1111/mec.15091] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 03/05/2019] [Accepted: 03/29/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Philip Lavretsky
- Department of Biological Sciences University of Texas at El Paso El Paso Texas
- Department of Biological Sciences Wright State University Dayton Ohio
- Department of Biology University of Miami Miami Florida
| | - Jeffrey M. DaCosta
- Biology Department Boston College Chestnut Hill Massachusetts
- Biology Department Boston College Boston Massachusetts
| | | | - Kevin G. McCracken
- Department of Biology University of Miami Miami Florida
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences University of Miami Miami Florida
- Human Genetics and Genomics Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami Florida
- Institute of Arctic Biology and University of Alaska Museum University of Alaska Fairbanks Fairbanks Alaska
| | - Jeffrey L. Peters
- Department of Biological Sciences Wright State University Dayton Ohio
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40
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Peñalba JV, Joseph L, Moritz C. Current geography masks dynamic history of gene flow during speciation in northern Australian birds. Mol Ecol 2019; 28:630-643. [PMID: 30561150 DOI: 10.1111/mec.14978] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 12/25/2022]
Abstract
Genome divergence is greatly influenced by gene flow during early stages of speciation. As populations differentiate, geographic barriers can constrain gene flow and so affect the dynamics of divergence and speciation. Current geography, specifically disjunction and continuity of ranges, is often used to predict the historical gene flow during the divergence process. We test this prediction in eight meliphagoid bird species complexes codistributed in four regions. These regions are separated by known biogeographical barriers across northern Australia and Papua New Guinea. We find that bird populations currently separated by terrestrial habitat barriers within Australia and marine barriers between Australia and Papua New Guinea have a range of divergence levels and probability of gene flow not associated with current range connectivity. Instead, geographic distance and historical range connectivity better predict divergence and probability of gene flow. In this dynamic environmental context, we also find support for a nonlinear decrease of the probability of gene flow during the divergence process. The probability of gene flow initially decreases gradually after a certain level of divergence is reached. Its decrease then accelerates until the probability is close to zero. This implies that although geographic connectivity may have more of an effect early in speciation, other factors associated with higher divergence may play a more important role in influencing gene flow midway through and later in speciation. Current geographic connectivity may then mislead inferences regarding potential for gene flow during speciation under a complex and dynamic history of geographic and reproductive isolation.
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Affiliation(s)
- Joshua V Peñalba
- Ecology and Evolution, Australian National University, Acton, ACT, Australia.,Centre for Biodiversity Analysis, Acton, ACT, Australia.,Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Canberra, ACT, Australia.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Germany
| | - Leo Joseph
- Centre for Biodiversity Analysis, Acton, ACT, Australia.,Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Canberra, ACT, Australia
| | - Craig Moritz
- Ecology and Evolution, Australian National University, Acton, ACT, Australia.,Centre for Biodiversity Analysis, Acton, ACT, Australia
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41
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Martin SH, Davey JW, Salazar C, Jiggins CD. Recombination rate variation shapes barriers to introgression across butterfly genomes. PLoS Biol 2019; 17:e2006288. [PMID: 30730876 PMCID: PMC6366726 DOI: 10.1371/journal.pbio.2006288] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 01/07/2019] [Indexed: 12/30/2022] Open
Abstract
Hybridisation and introgression can dramatically alter the relationships among groups of species, leading to phylogenetic discordance across the genome and between populations. Introgression can also erode species differences over time, but selection against introgression at certain loci acts to maintain postmating species barriers. Theory predicts that species barriers made up of many loci throughout the genome should lead to a broad correlation between introgression and recombination rate, which determines the extent to which selection on deleterious foreign alleles will affect neutral alleles at physically linked loci. Here, we describe the variation in genealogical relationships across the genome among three species of Heliconius butterflies: H. melpomene (mel), H. cydno (cyd), and H. timareta (tim), using whole genomes of 92 individuals, and ask whether this variation can be explained by heterogeneous barriers to introgression. We find that species relationships vary predictably at the chromosomal scale. By quantifying recombination rate and admixture proportions, we then show that rates of introgression are predicted by variation in recombination rate. This implies that species barriers are highly polygenic, with selection acting against introgressed alleles across most of the genome. In addition, long chromosomes, which have lower recombination rates, produce stronger barriers on average than short chromosomes. Finally, we find a consistent difference between two species pairs on either side of the Andes, which suggests differences in the architecture of the species barriers. Our findings illustrate how the combined effects of hybridisation, recombination, and natural selection, acting at multitudes of loci over long periods, can dramatically sculpt the phylogenetic relationships among species.
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Affiliation(s)
- Simon H. Martin
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - John W. Davey
- Department of Biology, University of York, York, United Kingdom
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogota, Colombia
| | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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42
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Pinharanda A, Rousselle M, Martin SH, Hanly JJ, Davey JW, Kumar S, Galtier N, Jiggins CD. Sexually dimorphic gene expression and transcriptome evolution provide mixed evidence for a fast-Z effect in Heliconius. J Evol Biol 2019; 32:194-204. [PMID: 30523653 PMCID: PMC6850379 DOI: 10.1111/jeb.13410] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 11/06/2018] [Accepted: 11/27/2018] [Indexed: 12/30/2022]
Abstract
Sex chromosomes have different evolutionary properties compared to autosomes due to their hemizygous nature. In particular, recessive mutations are more readily exposed to selection, which can lead to faster rates of molecular evolution. Here, we report patterns of gene expression and molecular evolution for a group of butterflies. First, we improve the completeness of the Heliconius melpomene reference annotation, a neotropical butterfly with a ZW sex determination system. Then, we analyse RNA from male and female whole abdomens and sequence female ovary and gut tissue to identify sex‐ and tissue‐specific gene expression profiles in H. melpomene. Using these expression profiles, we compare (a) sequence divergence and polymorphism; (b) the strength of positive and negative selection; and (c) rates of adaptive evolution, for Z and autosomal genes between two species of Heliconius butterflies, H. melpomene and H. erato. We show that the rate of adaptive substitutions is higher for Z than autosomal genes, but contrary to expectation, it is also higher for male‐biased than female‐biased genes. Additionally, we find no significant increase in the rate of adaptive evolution or purifying selection on genes expressed in ovary tissue, a heterogametic‐specific tissue. Our results contribute to a growing body of literature from other ZW systems that also provide mixed evidence for a fast‐Z effect where hemizygosity influences the rate of adaptive substitutions.
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Affiliation(s)
- Ana Pinharanda
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Marjolaine Rousselle
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Joe J Hanly
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - John W Davey
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Biology, University of York, York, UK
| | - Sujai Kumar
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nicolas Galtier
- Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK
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43
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Rieseberg L, Geraldes A, Belkin SE, Chambers KE, Kane N. Editorial 2019. Mol Ecol 2019; 28:1-28. [DOI: 10.1111/mec.14976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Payseur BA, Presgraves DC, Filatov DA. Introduction: Sex chromosomes and speciation. Mol Ecol 2018; 27:3745-3748. [PMID: 30086196 DOI: 10.1111/mec.14828] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Bret A Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin
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45
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Van Belleghem SM, Baquero M, Papa R, Salazar C, McMillan WO, Counterman BA, Jiggins CD, Martin SH. Patterns of Z chromosome divergence among Heliconius species highlight the importance of historical demography. Mol Ecol 2018; 27:3852-3872. [PMID: 29569384 PMCID: PMC6151167 DOI: 10.1111/mec.14560] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/14/2018] [Accepted: 02/20/2018] [Indexed: 12/31/2022]
Abstract
Sex chromosomes are disproportionately involved in reproductive isolation and adaptation. In support of such a “large‐X” effect, genome scans between recently diverged populations and species pairs often identify distinct patterns of divergence on the sex chromosome compared to autosomes. When measures of divergence between populations are higher on the sex chromosome compared to autosomes, such patterns could be interpreted as evidence for faster divergence on the sex chromosome, that is “faster‐X”, barriers to gene flow on the sex chromosome. However, demographic changes can strongly skew divergence estimates and are not always taken into consideration. We used 224 whole‐genome sequences representing 36 populations from two Heliconius butterfly clades (H. erato and H. melpomene) to explore patterns of Z chromosome divergence. We show that increased divergence compared to equilibrium expectations can in many cases be explained by demographic change. Among Heliconius erato populations, for instance, population size increase in the ancestral population can explain increased absolute divergence measures on the Z chromosome compared to the autosomes, as a result of increased ancestral Z chromosome genetic diversity. Nonetheless, we do identify increased divergence on the Z chromosome relative to the autosomes in parapatric or sympatric species comparisons that imply postzygotic reproductive barriers. Using simulations, we show that this is consistent with reduced gene flow on the Z chromosome, perhaps due to greater accumulation of incompatibilities. Our work demonstrates the importance of taking demography into account to interpret patterns of divergence on the Z chromosome, but nonetheless provides evidence to support the Z chromosome as a strong barrier to gene flow in incipient Heliconius butterfly species.
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Affiliation(s)
- Steven M Van Belleghem
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA.,Department of Biology, Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras, Puerto Rico.,Smithsonian Tropical Research Institute, Apartado, Panamá, Panama
| | - Margarita Baquero
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Riccardo Papa
- Department of Biology, Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Carrera, Bogota, Colombia
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Apartado, Panamá, Panama
| | - Brian A Counterman
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge, UK
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