1
|
Luo M, Hu J. Alternative splicing in parallel evolution and the evolutionary potential in sticklebacks. J Anim Ecol 2024. [PMID: 39056271 DOI: 10.1111/1365-2656.14157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 06/28/2024] [Indexed: 07/28/2024]
Abstract
Repeatability of adaptation to similar environments provides opportunity to evaluate the predictability of natural selection. While many studies have investigated gene expression differences between populations adapted to contrasting environments, the role of post-transcriptional processes such as alternative splicing has rarely been evaluated in the context of parallel adaptation. To address the aforementioned knowledge gap, we reanalysed transcriptomic data from three pairs of threespine stickleback (Gasterosteus aculeatus) ecotypes adapted to marine or freshwater environment. First, we identified genes with repeated expression or splicing divergence across ecotype pairs, and compared the genetic architecture and biological processes between parallelly expressed and parallelly spliced loci. Second, we analysed the extent to which parallel adaptation was reflected at gene expression and alternative splicing levels. Finally, we tested how the two axes of transcriptional variation differed in their potential for evolutionary change. Although both repeated differential splicing and differential expression across ecotype pairs showed tendency for parallel divergence, the degree of parallelism was lower for splicing than expression. Furthermore, parallel divergences in splicing and expression were likely to be associated with distinct cis-regulatory genetic variants and functionally unique set of genes. Finally, we found that parallelly spliced genes showed higher nucleotide diversity than parallelly expressed genes, indicating splicing is less susceptible to genetic variation erosion during parallel adaptation. Our results provide novel insight into the role of splicing in parallel adaptation, and underscore the contribution of splicing to the evolutionary potential of wild populations under environmental change.
Collapse
Affiliation(s)
- Man Luo
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| |
Collapse
|
2
|
Schmidt TL, Endersby-Harshman NM, van Rooyen ARJ, Katusele M, Vinit R, Robinson LJ, Laman M, Karl S, Hoffmann AA. Global, asynchronous partial sweeps at multiple insecticide resistance genes in Aedes mosquitoes. Nat Commun 2024; 15:6251. [PMID: 39048545 PMCID: PMC11269687 DOI: 10.1038/s41467-024-49792-y] [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: 12/20/2023] [Accepted: 06/19/2024] [Indexed: 07/27/2024] Open
Abstract
Aedes aegypti (yellow fever mosquito) and Ae. albopictus (Asian tiger mosquito) are globally invasive pests that confer the world's dengue burden. Insecticide-based management has led to the evolution of insecticide resistance in both species, though the genetic architecture and geographical spread of resistance remains incompletely understood. This study investigates partial selective sweeps at resistance genes on two chromosomes and characterises their spread across populations. Sweeps at the voltage-sensitive sodium channel (VSSC) gene on chromosome 3 correspond to one resistance-associated nucleotide substitution in Ae. albopictus and three in Ae. aegypti, including two substitutions at the same nucleotide position (F1534C) that have evolved and spread independently. In Ae. aegypti, we also identify partial sweeps at a second locus on chromosome 2. This locus contains 15 glutathione S-transferase (GST) epsilon class genes with significant copy number variation among populations and where three distinct genetic backgrounds have spread across the Indo-Pacific region, the Americas, and Australia. Local geographical patterns and linkage networks indicate VSSC and GST backgrounds probably spread at different times and interact locally with different genes to produce resistance phenotypes. These findings highlight the rapid global spread of resistance and are evidence for the critical importance of GST genes in resistance evolution.
Collapse
Affiliation(s)
- Thomas L Schmidt
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Australia.
| | | | | | - Michelle Katusele
- PNG Institute of Medical Research, Madang, Madang Province, Papua New Guinea
| | - Rebecca Vinit
- PNG Institute of Medical Research, Madang, Madang Province, Papua New Guinea
| | - Leanne J Robinson
- PNG Institute of Medical Research, Madang, Madang Province, Papua New Guinea
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, Queensland, Australia
| | - Moses Laman
- PNG Institute of Medical Research, Madang, Madang Province, Papua New Guinea
| | - Stephan Karl
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, Queensland, Australia
- Burnet Institute of Medical Research, Melbourne, Victoria, Australia
| | - Ary A Hoffmann
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Australia
| |
Collapse
|
3
|
Bohutínská M, Peichel CL. Divergence time shapes gene reuse during repeated adaptation. Trends Ecol Evol 2024; 39:396-407. [PMID: 38155043 DOI: 10.1016/j.tree.2023.11.007] [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: 08/10/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
When diverse lineages repeatedly adapt to similar environmental challenges, the extent to which the same genes are involved (gene reuse) varies across systems. We propose that divergence time among lineages is a key factor driving this variability: as lineages diverge, the extent of gene reuse should decrease due to reductions in allele sharing, functional differentiation among genes, and restructuring of genome architecture. Indeed, we show that many genomic studies of repeated adaptation find that more recently diverged lineages exhibit higher gene reuse during repeated adaptation, but the relationship becomes less clear at older divergence time scales. Thus, future research should explore the factors shaping gene reuse and their interplay across broad divergence time scales for a deeper understanding of evolutionary repeatability.
Collapse
Affiliation(s)
- Magdalena Bohutínská
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland; Department of Botany, Faculty of Science, Charles University, Prague, 12800, Czech Republic.
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland
| |
Collapse
|
4
|
Wang S, Girardello M, Zhang W. Potential and progress of studying mountain biodiversity by means of butterfly genetics and genomics. J Genet Genomics 2024; 51:292-301. [PMID: 37302475 DOI: 10.1016/j.jgg.2023.06.001] [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: 01/10/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023]
Abstract
Mountains are rich in biodiversity, and butterflies are species-rich and have a good ecological and evolutionary research foundation. This review addresses the potential and progress of studying mountain biodiversity using butterflies as a model. We discuss the uniqueness of mountain ecosystems, factors influencing the distribution of mountain butterflies, representative genetic and evolutionary models in butterfly research, and evolutionary studies of mountain biodiversity involving butterfly genetics and genomics. Finally, we demonstrate the necessity of studying mountain butterflies and propose future perspectives. This review provides insights for studying the biodiversity of mountain butterflies as well as a summary of research methods for reference.
Collapse
Affiliation(s)
- Shuting Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Marco Girardello
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group, Faculdade de Ciências Agrárias e do Ambiente, Universidade dos Açores, 9700-042 Angra do Heroísmo, Terceira, Portugal
| | - Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
| |
Collapse
|
5
|
Booker TR, Yeaman S, Whiting JR, Whitlock MC. The WZA: A window-based method for characterizing genotype-environment associations. Mol Ecol Resour 2024; 24:e13768. [PMID: 36785926 DOI: 10.1111/1755-0998.13768] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 02/15/2023]
Abstract
Genotype-environment association (GEA) studies have the potential to identify the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features of the environment. Genetic markers with extreme evidence of correlation with the environment are presumed to be tagging the location of alleles that contribute to local adaptation. In this study, we propose a new method for GEA studies called the Weighted-Z Analysis (WZA) that combines information from closely linked sites into analysis windows in a way that was inspired by methods for calculating FST . Performing GEA methods in analysis windows has the advantage that it takes advantage of the increased linkage disequilibrium expected surrounding sites subject to local adaptation. We analyse simulations modelling local adaptation to heterogeneous environments to compare the WZA with existing methods. In the majority of cases we tested, the WZA either outperformed single-SNP (single nucleotide polymorphism)-based approaches or performed similarly. In particular, the WZA outperformed individual SNP approaches when a small number of individuals or demes were sampled. Particularly troubling, we found that some GEA methods exhibit very high false positive rates. We applied the WZA to previously published data from lodgepole pine and identified candidate loci that were identified in the original study alongside numerous loci that were not found in the original study.
Collapse
Affiliation(s)
- Tom R Booker
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - James R Whiting
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Michael C Whitlock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
6
|
Parvizi E, Vaughan AL, Dhami MK, McGaughran A. Genomic signals of local adaptation across climatically heterogenous habitats in an invasive tropical fruit fly (Bactrocera tryoni). Heredity (Edinb) 2024; 132:18-29. [PMID: 37903919 PMCID: PMC10798995 DOI: 10.1038/s41437-023-00657-y] [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: 02/14/2023] [Revised: 09/21/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
Local adaptation plays a key role in the successful establishment of pest populations in new environments by enabling them to tolerate novel biotic and abiotic conditions experienced outside their native range. However, the genomic underpinnings of such adaptive responses remain unclear, especially for agriculturally important pests. We investigated population genomic signatures in the tropical/subtropical Queensland fruit fly, Bactrocera tryoni, which has an expanded range encompassing temperate and arid zones in Australia, and tropical zones in the Pacific Islands. Using reduced representation sequencing data from 28 populations, we detected allele frequency shifts associated with the native/invasive status of populations and identified environmental factors that have likely driven population differentiation. We also determined that precipitation, temperature, and geographic variables explain allelic shifts across the distribution range of B. tryoni. We found spatial heterogeneity in signatures of local adaptation across various climatic conditions in invaded areas. Specifically, disjunct invasive populations in the tropical Pacific Islands and arid zones of Australia were characterised by multiple significantly differentiated single nucleotide polymorphisms (SNPs), some of which were associated with genes with well-understood function in environmental stress (e.g., heat and desiccation) response. However, invasive populations in southeast Australian temperate zones showed higher gene flow with the native range and lacked a strong local adaptive signal. These results suggest that population connectivity with the native range has differentially affected local adaptive patterns in different invasive populations. Overall, our findings provide insights into the evolutionary underpinnings of invasion success of an important horticultural pest in climatically distinct environments.
Collapse
Affiliation(s)
- Elahe Parvizi
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Amy L Vaughan
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Manpreet K Dhami
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Angela McGaughran
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand.
| |
Collapse
|
7
|
Zhao Y, Su C, He B, Nie R, Wang Y, Ma J, Song J, Yang Q, Hao J. Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome. Nat Commun 2023; 14:8190. [PMID: 38081828 PMCID: PMC10713551 DOI: 10.1038/s41467-023-44023-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Parnassius glacialis is a typical "Out of the QTP" alpine butterfly that originated on the Qinghai-Tibet Plateau (QTP) and dispersed into relatively low-altitude mountainous. Here we assemble a chromosome-level genome of P. glacialis and resequence 9 populations in order to explore the genome evolution and local adaptation of this species. These results indicated that the rapid accumulation and slow unequal recombination of transposable elements (TEs) contributed to the formation of its large genome. Several ribosomal gene families showed extensive expansion and selective evolution through transposon-mediated processed pseudogenes. Additionally, massive structural variations (SVs) of TEs affected the genetic differentiation of low-altitude populations. These low-altitude populations might have experienced a genetic bottleneck in the past and harbor genes with selective signatures which may be responsible for the potential adaptation to low-altitude environments. These results provide a foundation for understanding genome evolution and local adaptation for "Out of the QTP" of P. glacialis.
Collapse
Affiliation(s)
- Youjie Zhao
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224, Yunnan, China
| | - Chengyong Su
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Bo He
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Ruie Nie
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Yunliang Wang
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Junye Ma
- State Key Laboratory of Palaeobiology and Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jingyu Song
- College of Animal Science, Shandong Agricultural University, Taian, 271000, China
| | - Qun Yang
- State Key Laboratory of Palaeobiology and Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China.
- Nanjing College, University of Chinese Academy of Sciences, Nanjing, 211135, China.
| | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
| |
Collapse
|
8
|
Cerca J. Understanding natural selection and similarity: Convergent, parallel and repeated evolution. Mol Ecol 2023; 32:5451-5462. [PMID: 37724599 DOI: 10.1111/mec.17132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
Parallel and convergent evolution offer some of the most compelling evidence for the significance of natural selection in evolution, as the emergence of similar adaptive solutions is unlikely to occur by random chance alone. However, these terms are often employed inconsistently, leading to misinterpretation and confusion, and recently proposed definitions have unintentionally diminished the emphasis on the evolution of similar adaptive solutions. Here, I examine various conceptual frameworks and definitions related to parallel and convergent evolution and propose a consolidated framework that enhances our comprehension of these evolutionary patterns. The primary aim of this framework is to harmonize the concepts of parallel and convergent evolution together with natural selection and the idea of similarity. Both concepts involve the evolution of similar adaptive solutions as a result of environmental challenges. The distinction lies in ancestral phenotypes. Parallel evolution takes place when the ancestral phenotypes (before selection) of the lineages are similar. Convergent evolution happens when the lineages have distinct ancestral phenotypes (before selection). Because an ancestral-based distinction will inevitably lead to cases where uncertainty in the distinction may arise, the framework includes a general term, repeated evolution, which can be used as a term applying to the evolution of similar phenotypes and genotypes as well as similar responses to environmental pressures. Based on the argument that genetic similarity may frequently arise without selection, the framework posits that the similarity of genetic sequences is not of great interest unless linked to the actions of natural selection or to the origins (mutation, standing genetic variation, gene flow) and locations of the similar sequences.
Collapse
Affiliation(s)
- José Cerca
- CEES - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| |
Collapse
|
9
|
Cerca J, Cotoras DD, Santander CG, Bieker VC, Hutchins L, Morin-Lagos J, Prada CF, Kennedy S, Krehenwinkel H, Rominger AJ, Meier J, Dimitrov D, Struck TH, Gillespie RG. Multiple paths toward repeated phenotypic evolution in the spiny-leg adaptive radiation (Tetragnatha; Hawai'i). Mol Ecol 2023; 32:4971-4985. [PMID: 37515430 DOI: 10.1111/mec.17082] [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: 12/08/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
The repeated evolution of phenotypes provides clear evidence for the role of natural selection in driving evolutionary change. However, the evolutionary origin of repeated phenotypes can be difficult to disentangle as it can arise from a combination of factors such as gene flow, shared ancestral polymorphisms or mutation. Here, we investigate the presence of these evolutionary processes in the Hawaiian spiny-leg Tetragnatha adaptive radiation, which includes four microhabitat-specialists or ecomorphs, with different body pigmentation and size (Green, Large Brown, Maroon, and Small Brown). We investigated the evolutionary history of this radiation using 76 newly generated low-coverage, whole-genome resequenced samples, along with phylogenetic and population genomic tools. Considering the Green ecomorph as the ancestral state, our results suggest that the Green ecomorph likely re-evolved once, the Large Brown and Maroon ecomorphs evolved twice and the Small Brown evolved three times. We found that the evolution of the Maroon and Small Brown ecomorphs likely involved ancestral hybridization events, while the Green and Large Brown ecomorphs likely evolved through novel mutations, despite a high rate of incomplete lineage sorting in the dataset. Our findings demonstrate that the repeated evolution of ecomorphs in the Hawaiian spiny-leg Tetragnatha is influenced by multiple evolutionary processes.
Collapse
Affiliation(s)
- José Cerca
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, Berkeley, California, USA
- Frontiers in Evolutionary Zoology, Natural History Museum, University of Oslo, Oslo, Norway
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Darko D Cotoras
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany
- Department of Entomology, California Academy of Sciences, San Francisco, California, USA
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Leke Hutchins
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, Berkeley, California, USA
| | - Jaime Morin-Lagos
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Carlos F Prada
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Tolima, Colombia
| | - Susan Kennedy
- Department of Biogeography, Trier University, Trier, Germany
| | | | - Andrew J Rominger
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
| | - Joana Meier
- Department of Zoology, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Sanger Institute, Hinxton, UK
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Torsten H Struck
- Frontiers in Evolutionary Zoology, Natural History Museum, University of Oslo, Oslo, Norway
| | - Rosemary G Gillespie
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, Berkeley, California, USA
| |
Collapse
|
10
|
Louis M, Korlević P, Nykänen M, Archer F, Berrow S, Brownlow A, Lorenzen ED, O'Brien J, Post K, Racimo F, Rogan E, Rosel PE, Sinding MHS, van der Es H, Wales N, Fontaine MC, Gaggiotti OE, Foote AD. Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters. Nat Commun 2023; 14:4020. [PMID: 37463880 DOI: 10.1038/s41467-023-39532-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats.
Collapse
Affiliation(s)
- Marie Louis
- Centre for Biological Diversity, Sir Harold Mitchell Building and Dyers Brae, University of St Andrews, St Andrews, KY16 9TH, Scotland, UK.
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands.
- Greenland Institute of Natural Resources, Kivioq 2, Nuuk, 3900, Greenland.
| | - Petra Korlević
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Milaja Nykänen
- Department of Environmental and Biological Sciences, PO Box 111, FI-80101, Joensuu, Finland
- School of Biological, Earth and Environmental Sciences, University College Cork, North Mall, Cork, Ireland
| | - Frederick Archer
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, NOAA, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Simon Berrow
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Atlantic Technological University, Dublin Road, H91 T8NW, Galway, Ireland
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Eline D Lorenzen
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Joanne O'Brien
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Atlantic Technological University, Dublin Road, H91 T8NW, Galway, Ireland
| | - Klaas Post
- Natural History Museum Rotterdam, Westzeedijk 345, 3015 AA, Rotterdam, Netherlands
| | - Fernando Racimo
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Emer Rogan
- School of Biological, Earth and Environmental Sciences, University College Cork, North Mall, Cork, Ireland
| | - Patricia E Rosel
- Marine Mammal and Turtle Division, Southeast Fisheries Science Center, NOAA, 646 Cajundome Boulevard, Lafayette, LA, 70506, USA
| | - Mikkel-Holger S Sinding
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Henry van der Es
- Natural History Museum Rotterdam, Westzeedijk 345, 3015 AA, Rotterdam, Netherlands
| | - Nathan Wales
- University of York, BioArCh, Environment Building, Wentworth Way, Heslington, York, YO10 5DD, UK
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
- MIVEGEC (Université de Montpellier, CNRS 5290, IRD 229) Institut de Recherche pour le Développement (IRD), F-34394, Montpellier, France
| | - Oscar E Gaggiotti
- Centre for Biological Diversity, Sir Harold Mitchell Building and Dyers Brae, University of St Andrews, St Andrews, KY16 9TH, Scotland, UK
| | - Andrew D Foote
- Department of Natural History, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway.
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316, Oslo, Norway.
| |
Collapse
|
11
|
Genome-wide parallelism underlies contemporary adaptation in urban lizards. Proc Natl Acad Sci U S A 2023; 120:e2216789120. [PMID: 36634133 PMCID: PMC9934206 DOI: 10.1073/pnas.2216789120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Urbanization drastically transforms landscapes, resulting in fragmentation, degradation, and the loss of local biodiversity. Yet, urban environments also offer opportunities to observe rapid evolutionary change in wild populations that survive and even thrive in these novel habitats. In many ways, cities represent replicated "natural experiments" in which geographically separated populations adaptively respond to similar selection pressures over rapid evolutionary timescales. Little is known, however, about the genetic basis of adaptive phenotypic differentiation in urban populations nor the extent to which phenotypic parallelism is reflected at the genomic level with signatures of parallel selection. Here, we analyzed the genomic underpinnings of parallel urban-associated phenotypic change in Anolis cristatellus, a small-bodied neotropical lizard found abundantly in both urbanized and forested environments. We show that phenotypic parallelism in response to parallel urban environmental change is underlain by genomic parallelism and identify candidate loci across the Anolis genome associated with this adaptive morphological divergence. Our findings point to polygenic selection on standing genetic variation as a key process to effectuate rapid morphological adaptation. Identified candidate loci represent several functions associated with skeletomuscular development, morphology, and human disease. Taken together, these results shed light on the genomic basis of complex morphological adaptations, provide insight into the role of contingency and determinism in adaptation to novel environments, and underscore the value of urban environments to address fundamental evolutionary questions.
Collapse
|
12
|
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] [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.
Collapse
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
| | | |
Collapse
|