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Pinsky ML, Clark RD, Bos JT. Coral Reef Population Genomics in an Age of Global Change. Annu Rev Genet 2023; 57:87-115. [PMID: 37384733 DOI: 10.1146/annurev-genet-022123-102748] [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] [Indexed: 07/01/2023]
Abstract
Coral reefs are both exceptionally biodiverse and threatened by climate change and other human activities. Here, we review population genomic processes in coral reef taxa and their importance for understanding responses to global change. Many taxa on coral reefs are characterized by weak genetic drift, extensive gene flow, and strong selection from complex biotic and abiotic environments, which together present a fascinating test of microevolutionary theory. Selection, gene flow, and hybridization have played and will continue to play an important role in the adaptation or extinction of coral reef taxa in the face of rapid environmental change, but research remains exceptionally limited compared to the urgent needs. Critical areas for future investigation include understanding evolutionary potential and the mechanisms of local adaptation, developing historical baselines, and building greater research capacity in the countries where most reef diversity is concentrated.
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Affiliation(s)
- Malin L Pinsky
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA;
| | - René D Clark
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
| | - Jaelyn T Bos
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
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2
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Bridle J, Hoffmann A. Understanding the biology of species' ranges: when and how does evolution change the rules of ecological engagement? Philos Trans R Soc Lond B Biol Sci 2022; 377:20210027. [PMID: 35184590 PMCID: PMC8859517 DOI: 10.1098/rstb.2021.0027] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Understanding processes that limit species' ranges has been a core issue in ecology and evolutionary biology for many decades, and has become increasingly important given the need to predict the responses of biological communities to rapid environmental change. However, we still have a poor understanding of evolution at range limits and its capacity to change the ecological 'rules of engagement' that define these communities, as well as the time frame over which this occurs. Here we link papers in the current volume to some key concepts involved in the interactions between evolutionary and ecological processes at species' margins. In particular, we separate hypotheses about species' margins that focus on hard evolutionary limits, which determine how genotypes interact with their environment, from those concerned with soft evolutionary limits, which determine where and when local adaptation can persist in space and time. We show how theoretical models and empirical studies highlight conditions under which gene flow can expand local limits as well as contain them. In doing so, we emphasize the complex interplay between selection, demography and population structure throughout a species' geographical and ecological range that determines its persistence in biological communities. However, despite some impressively detailed studies on range limits, particularly in invertebrates and plants, few generalizations have emerged that can predict evolutionary responses at ecological margins. We outline some directions for future work such as considering the impact of structural genetic variants and metapopulation structure on limits, and the interaction between range limits and the evolution of mating systems and non-random dispersal. This article is part of the theme issue 'Species' ranges in the face of changing environments (Part II)'.
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Affiliation(s)
- Jon Bridle
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Ary Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
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3
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Alabi N, Wu Y, Bossdorf O, Rieseberg LH, Colautti RI. Genome Report: A draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics. G3-GENES GENOMES GENETICS 2021; 11:6380431. [PMID: 34599816 PMCID: PMC8664459 DOI: 10.1093/g3journal/jkab339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 09/10/2021] [Indexed: 11/24/2022]
Abstract
The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here, we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara and Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC3-3-20) collected from the native range near Venice, Italy, and sequenced paired-end and mate pair libraries at ∼70 × coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121 Mb; L50 = 2) with 99.7% of the 1.1 Gb genome mapping to scaffolds of at least 50 Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe, we found that almost one-third of BUSCO genes (390/1440) mapped to two or more scaffolds despite <2% genome-wide average heterozygosity. The continuity and gene space quality of our draft assembly will enable molecular and functional genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation strategies.
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Affiliation(s)
- Nikolay Alabi
- Biology Department, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Yihan Wu
- Biology Department, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Oliver Bossdorf
- Institute of Ecology and Evolution, University of Tübingen, 72074 Tübingen, Germany
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Robert I Colautti
- Biology Department, Queen's University, Kingston, Ontario K7L 3N6, Canada
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4
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Chen Y, Hou G, Jing M, Teng H, Liu Q, Yang X, Wang Y, Qu J, Shi C, Lu L, Zhang J, Zhang Y. Genomic analysis unveils mechanisms of northward invasion and signatures of plateau adaptation in the Asian house rat. Mol Ecol 2021; 30:6596-6610. [PMID: 34564921 DOI: 10.1111/mec.16194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 07/21/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022]
Abstract
The Asian house rat (AHR), Rattus tanezumi, has recently invaded the northern half of China. The AHR is a highly adaptive rat species that has also successfully conquered the Qinghai-Tibet Plateau (QTP) and replaced the brown rat (BR), R. norvegicus, at the edge of the QTP. Here, we assembled a draft genome of the AHR and explored the mechanisms of its northward invasion and the genetic basis underlying plateau adaptation in this species. Population genomic analyses revealed that the northwardly invasive AHRs consisted of two independent and genetically distinct populations which might result from multiple independent primary invasion events. One invasive population exhibited reduced genetic diversity and distinct population structure compared with its source population, while the other displayed preserved genetic polymorphisms and little genetic differentiation from its source population. Genes involved in G-protein coupled receptors and carbohydrate metabolism may contribute to the local adaptation of northern AHRs. In particular, RTN4 was identified as a key gene for AHRs in the QTP that favours adaptation to high-altitude hypoxia. Coincidently, the physiological performance and transcriptome profiles of hypoxia-exposed rats both showed better hypoxia adaptation in AHRs than in BRs that failed to colonize the heart of the QTP, which may have facilitated the replacement of the BR population by the invading AHRs at the edge of the QTP. This study provides profound insights into the multiple origins of the northwardly invasive AHR and the great tolerance to hypoxia in this species.
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Affiliation(s)
- Yi Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Guanmei Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Meidong Jing
- School of Life Sciences, Nantong University, Nantong, China
| | - Huajing Teng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Quansheng Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xingen Yang
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Institute of Plant Protection, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Yong Wang
- Dongting Lake Station for Wetland Ecosystem Research, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Jiapeng Qu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai, China
| | - Chengmin Shi
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Liang Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianxu Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Yaohua Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
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Flanagan BA, Krueger-Hadfield SA, Murren CJ, Nice CC, Strand AE, Sotka EE. Founder effects shape linkage disequilibrium and genomic diversity of a partially clonal invader. Mol Ecol 2021; 30:1962-1978. [PMID: 33604965 DOI: 10.1111/mec.15854] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/18/2021] [Accepted: 02/01/2021] [Indexed: 12/20/2022]
Abstract
The genomic variation of an invasive species may be affected by complex demographic histories and evolutionary changes during the invasion. Here, we describe the relative influence of bottlenecks, clonality, and population expansion in determining genomic variability of the widespread red macroalga Agarophyton vermiculophyllum. Its introduction from mainland Japan to the estuaries of North America and Europe coincided with shifts from predominantly sexual to partially clonal reproduction and rapid adaptive evolution. A survey of 62,285 SNPs for 351 individuals from 35 populations, aligned to 24 chromosome-length scaffolds indicate that linkage disequilibrium (LD), observed heterozygosity (Ho ), Tajima's D, and nucleotide diversity (Pi) were greater among non-native than native populations. Evolutionary simulations indicate LD and Tajima's D were consistent with a severe population bottleneck. Also, the increased rate of clonal reproduction in the non-native range could not have produced the observed patterns by itself but may have magnified the bottleneck effect on LD. Elevated marker diversity in the genetic source populations could have contributed to the increased Ho and Pi observed in the non-native range. We refined the previous invasion source region to a ~50 km section of northeastern Honshu Island. Outlier detection methods failed to reveal any consistently differentiated loci shared among invaded regions, probably because of the complex A. vermiculophyllum demographic history. Our results reinforce the importance of demographic history, specifically founder effects, in driving genomic variation of invasive populations, even when localized adaptive evolution and reproductive system shifts are observed.
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Affiliation(s)
- Ben A Flanagan
- Department of Biology, College of Charleston, Charleston, SC, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stacy A Krueger-Hadfield
- Department of Biology, College of Charleston, Charleston, SC, USA.,Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Chris C Nice
- Department of Biology, Population and Conservation Biology Program, Texas State University, San Marcos, TX, USA
| | - Allan E Strand
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - Erik E Sotka
- Department of Biology, College of Charleston, Charleston, SC, USA
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Wegner KM, Lokmer A, John U. Genomic and Transcriptomic Differentiation of Independent Invasions of the Pacific Oyster Crassostrea gigas. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.567049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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7
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Popovic I, Matias AMA, Bierne N, Riginos C. Twin introductions by independent invader mussel lineages are both associated with recent admixture with a native congener in Australia. Evol Appl 2020; 13:515-532. [PMID: 32431733 PMCID: PMC7045716 DOI: 10.1111/eva.12857] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 06/27/2019] [Accepted: 07/24/2019] [Indexed: 01/04/2023] Open
Abstract
Introduced species can impose profound impacts on the evolution of receiving communities with which they interact. If native and introduced taxa remain reproductively semi-isolated, human-mediated secondary contact may promote genetic exchange across newly created hybrid zones, potentially impacting native genetic diversity and invasive species spread. Here, we investigate the contributions of recent divergence histories and ongoing (post-introduction) gene flow between the invasive marine mussel, Mytilus galloprovincialis, and a morphologically indistinguishable and taxonomically contentious native Australian taxon, Mytilus planulatus. Using transcriptome-wide markers, we demonstrate that two contemporary M. galloprovincialis introductions into south-eastern Australia originate from genetically divergent lineages from its native range in the Mediterranean Sea and Atlantic Europe, where both introductions have led to repeated instances of admixture between introduced and endemic populations. Through increased genome-wide resolution of species relationships, combined with demographic modelling, we validate that mussels sampled in Tasmania are representative of the endemic Australian taxon (M. planulatus), but share strong genetic affinities to M. galloprovincialis. Demographic inferences indicate late-Pleistocene divergence times and historical gene flow between the Tasmanian endemic lineage and northern M. galloprovincialis, suggesting that native and introduced taxa have experienced a period of historical isolation of at least 100,000 years. Our results demonstrate that many genomic loci and sufficient sampling of closely related lineages in both sympatric (e.g. Australian populations) and allopatric (e.g. northern hemisphere Mytilus taxa) ranges are necessary to accurately (a) interpret patterns of intraspecific differentiation and to (b) distinguish contemporary invasive introgression from signatures left by recent divergence histories in high dispersal marine species. More broadly, our study fills a significant gap in systematic knowledge of native Australian biodiversity and sheds light on the intrinsic challenges for invasive species research when native and introduced species boundaries are not well defined.
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Affiliation(s)
- Iva Popovic
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
| | | | - Nicolas Bierne
- Institut des Sciences de l’EvolutionUMR 5554CNRS‐IRD‐EPHE‐UMUniversité de MontpellierMontpellierFrance
| | - Cynthia Riginos
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
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Hudson J, Johannesson K, McQuaid CD, Rius M. Secondary contacts and genetic admixture shape colonization by an amphiatlantic epibenthic invertebrate. Evol Appl 2020; 13:600-612. [PMID: 32431738 PMCID: PMC7045719 DOI: 10.1111/eva.12893] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 08/30/2019] [Accepted: 10/16/2019] [Indexed: 01/03/2023] Open
Abstract
Research on the genetics of invasive species often focuses on patterns of genetic diversity and population structure within the introduced range. However, a growing body of literature is demonstrating the need to study how native genotypes affect both ecological and evolutionary mechanisms within the introduced range. Here, we used genotyping-by-sequencing to study both native and introduced ranges of the amphiatlantic marine invertebrate Ciona intestinalis. A previous study using microsatellites analysed samples collected along the Swedish west coast and showed the presence of genetically distinct lineages in deep and shallow waters. Using 1,653 single nucleotide polymorphisms (SNPs) from newly collected samples (285 individuals), we first confirmed the presence of this depth-defined genomic divergence along the Swedish coast. We then used approximate Bayesian computation to infer the historical relationship among sites from the North Sea, the English Channel and the northwest Atlantic and found evidence of ancestral divergence between individuals from deep waters off Sweden and individuals from the English Channel. This divergence was followed by a secondary contact that led to a genetic admixture between the ancestral populations (i.e., deep Sweden and English Channel), which originated the genotypes found in shallow Sweden. We then revealed that the colonization of C. intestinalis in the northwest Atlantic was as a result of an admixture between shallow Sweden and the English Channel genotypes across the introduced range. Our results showed the presence of both past and recent genetic admixture events that together may have promoted the successful colonizations of C. intestinalis. Our study suggests that secondary contacts potentially reshape the evolutionary trajectories of invasive species through the promotion of intraspecific hybridization and by altering both colonization patterns and their ecological effects in the introduced range.
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Affiliation(s)
- Jamie Hudson
- School of Ocean and Earth ScienceNational Oceanography Centre SouthamptonUniversity of SouthamptonSouthamptonUK
| | - Kerstin Johannesson
- Department of Marine SciencesTjärnö Marine LaboratoryUniversity of GothenburgStrömstadSweden
| | - Christopher D. McQuaid
- Department of Zoology and EntomologyCoastal Research GroupRhodes UniversityGrahamstownSouth Africa
| | - Marc Rius
- School of Ocean and Earth ScienceNational Oceanography Centre SouthamptonUniversity of SouthamptonSouthamptonUK
- Department of ZoologyCentre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgAuckland ParkSouth Africa
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