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Yamasaki T, Kobayashi Y. Evolving dispersal ability causes rapid adaptive radiation. Sci Rep 2024; 14:15734. [PMID: 38977746 PMCID: PMC11231149 DOI: 10.1038/s41598-024-66435-w] [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: 09/14/2023] [Accepted: 07/01/2024] [Indexed: 07/10/2024] Open
Abstract
Despite a long history of research since Darwin, the mechanism underlying rapid adaptive radiation remains poorly understood. All theories constructed to date require special assumptions, so none can comprehensively explain actual cases found in wide-ranging taxonomic groups. Here, we propose a simple theoretical solution to this problem. Namely, we extend the classical archipelago model of adaptive radiation into a more realistic model by adding one assumption, namely, the evolvability of dispersal ability, which is well supported empirically. Our individual-based simulations with evolvable dispersal ability showed that environmental heterogeneity among islands (or island-like habitats) led to an evolutionary decrease in dispersal ability. However, when islands are rather evenly distributed, as is often the case in actual archipelagos where adaptive radiation has been reported, the decline in dispersal ability that began in some island populations was quickly halted by the continuous influx of immigrants from other islands. The process of reduction in dispersal ability in these island populations was resumed almost synchronously when the dispersal ability began to decrease on the final island, which had maintained high dispersal ability and continued to release migrants for the longest duration. Then, a rapid loss of dispersal ability followed in all island populations. In short, the frequent simultaneous evolution of multiple allopatric incipient species was an inevitable consequence of the properties of ordinary archipelagos in our simulations. This study strongly suggests that the seemingly complex process of rapid radiation is driven by a simple mechanism of evolutionary reduction in dispersal ability.
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Affiliation(s)
- Takeshi Yamasaki
- Yamashina Institute for Ornithology, 115 Konoyama, Abiko, Chiba, 270-1145, Japan.
| | - Yutaka Kobayashi
- School of Economics and Management, Kochi University of Technology, 2-22 Eikokuji-Cho, Kochi, 780-8515, Japan
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2
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Mackintosh C, Scott MF, Reuter M, Pomiankowski A. Locally adaptive inversions in structured populations. Genetics 2024; 227:iyae073. [PMID: 38709495 DOI: 10.1093/genetics/iyae073] [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: 01/27/2024] [Revised: 04/05/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
Inversions have been proposed to facilitate local adaptation, by linking together locally coadapted alleles at different loci. Prior work addressing this question theoretically has considered the spread of inversions in "continent-island" scenarios in which there is a unidirectional flow of maladapted migrants into the island population. In this setting, inversions capturing locally adaptive haplotypes are most likely to invade when selection is weak, because stronger local selection (i) more effectively purges maladaptive alleles and (ii) generates linkage disequilibrium between adaptive alleles, thus lessening the advantage of inversions. We show this finding only holds under limited conditions by studying the establishment of inversions in a more general two-deme model, which explicitly considers the dynamics of allele frequencies in both populations linked by bidirectional migration. In this model, the level of symmetry between demes can be varied from complete asymmetry (continent-island) to complete symmetry. For symmetric selection and migration, strong selection increases the allele frequency divergence between demes thereby increasing the frequency of maladaptive alleles in migrants, favoring inversions-the opposite of the pattern seen in the asymmetric continent-island scenario. We also account for the likelihood that a new inversion captures an adaptive haplotype in the first instance. When considering the combined process of capture and invasion in "continent island" and symmetric scenarios, relatively strong selection increases inversion establishment probability. Migration must also be low enough that the inversion is likely to capture an adaptive allele combination, but not so low as to eliminate the inversion's advantage. Overall, our analysis suggests that inversions are likely to harbor larger effect alleles that experience relatively strong selection.
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Affiliation(s)
- Carl Mackintosh
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
- CoMPLEX, University College London, Gower Street, London WC1E 6BT, UK
- CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff 29680, France
- Sorbonne Universités, UPMC Université Paris VI, Roscoff 29680, France
| | - Michael F Scott
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Max Reuter
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Andrew Pomiankowski
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
- CoMPLEX, University College London, Gower Street, London WC1E 6BT, UK
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3
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Montalvo LD, Kimball RT, Austin JD, Robinson SK. Unraveling the genomic landscape of Campylorhynchus wrens along western Ecuador's precipitation gradient: Insights into hybridization, isolation by distance, and isolation by the environment. Ecol Evol 2024; 14:e11661. [PMID: 38994212 PMCID: PMC11237350 DOI: 10.1002/ece3.11661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 05/31/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024] Open
Abstract
Environmental gradients have the potential to influence genetic differentiation among populations ultimately leading to allopatric speciation. However, environmental gradients can also facilitate hybridization between closely related taxa. We investigated a putative hybrid zone in western Ecuador, involving two polytypic wren species (Aves: Troglodytidae), Campylorhynchus zonatus and C. fasciatus. Our study addressed two primary questions: (1) Is there evidence of population structure and genetic admixture between these taxa in western Ecuador? and (2) What are the relative contributions of isolation by distance and isolation by the environment to the observed genetic differentiation along the environmental gradient in this region? We analyzed 4409 single-nucleotide polymorphisms (SNPs) from 112 blood samples sequenced using ddRadSeq and a de novo assembly. The optimum number of genetic clusters ranged from 2 to 4, aligning with geographic origins, known phylogenetics, and physical or ecological constraints. We observed notable transitions in admixture proportions along the environmental gradient in western Ecuador between C. z. brevirostris and the northern and southern genetic clusters of C. f. pallescens. Genetic differentiation between the two C. f. pallescens populations could be attributed to an unreported potential physical barrier in central western Ecuador, where the proximity of the Andes to the coastline restricts lowland habitats, limiting dispersal and gene flow, especially among dry-habitat specialists. The observed admixture in C. f. pallescens suggests that this subspecies may be a hybrid between C. z. brevirostris and C. fasciatus, with varying degrees of admixture in western Ecuador and northwestern Peru. We found evidence of isolation by distance, while isolation by the environment was less pronounced but still significant for annual mean precipitation and precipitation seasonality. This study enhances our understanding of avian population genomics in tropical regions.
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Affiliation(s)
- Luis Daniel Montalvo
- Florida Museum of Natural History University of Florida Gainesville Florida USA
- Department of Biology University of Florida Gainesville Florida USA
| | | | - James D Austin
- Department of Wildlife Ecology and Conservation University of Florida Gainesville Florida USA
| | - Scott K Robinson
- Florida Museum of Natural History University of Florida Gainesville Florida USA
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4
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Bourret A, Leung C, Puncher GN, Le Corre N, Deslauriers D, Skanes K, Bourdages H, Cassista-Da Ros M, Walkusz W, Jeffery NW, Stanley RRE, Parent GJ. Diving into broad-scale and high-resolution population genomics to decipher drivers of structure and climatic vulnerability in a marine invertebrate. Mol Ecol 2024:e17448. [PMID: 38946210 DOI: 10.1111/mec.17448] [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: 01/31/2024] [Revised: 06/11/2024] [Accepted: 06/19/2024] [Indexed: 07/02/2024]
Abstract
Species with widespread distributions play a crucial role in our understanding of climate change impacts on population structure. In marine species, population structure is often governed by both high connectivity potential and selection across strong environmental gradients. Despite the complexity of factors influencing marine populations, studying species with broad distribution can provide valuable insights into the relative importance of these factors and the consequences of climate-induced alterations across environmental gradients. We used the northern shrimp Pandalus borealis and its wide latitudinal distribution to identify current drivers of population structure and predict the species' vulnerability to climate change. A total of 1514 individuals sampled across 24° latitude were genotyped at high geographic (54 stations) and genetic (14,331 SNPs) resolutions to assess genetic variation and environmental correlations. Four populations were identified in addition to finer substructure associated with local adaptation. Geographic patterns of neutral population structure reflected predominant oceanographic currents, while a significant proportion of the genetic variation was associated with gradients in salinity and temperature. Adaptive landscapes generated using climate projections suggest a larger genomic offset in the southern extent of the P. borealis range, where shrimp had the largest adaptive standing genetic variation. Our genomic results combined with recent observations point to further deterioration in southern regions and an impending vulnerable status in the regions at higher latitudes for P. borealis. They also provide rare insights into the drivers of population structure and climatic vulnerability of a widespread meroplanktonic species, which is crucial to understanding future challenges associated with invertebrates essential to ecosystem functioning.
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Affiliation(s)
- Audrey Bourret
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, Quebec, Canada
| | - Christelle Leung
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, Quebec, Canada
| | - Gregory N Puncher
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, Nova Scotia, Canada
| | - Nicolas Le Corre
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - David Deslauriers
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, Rimouski, Quebec, Canada
| | - Katherine Skanes
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Hugo Bourdages
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, Quebec, Canada
| | - Manon Cassista-Da Ros
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, Nova Scotia, Canada
| | - Wojciech Walkusz
- Freshwater Institute, Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | - Nicholas W Jeffery
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, Nova Scotia, Canada
| | - Ryan R E Stanley
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, Nova Scotia, Canada
| | - Geneviève J Parent
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, Quebec, Canada
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5
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Barraclough TG. Does selection favour the maintenance of porous species boundaries? J Evol Biol 2024; 37:616-627. [PMID: 38599591 DOI: 10.1093/jeb/voae030] [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: 08/04/2023] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 04/12/2024]
Abstract
The endpoint of speciation has been viewed as complete isolation and the absence of gene flow between species. If the influx of genes from another species is maladaptive because species have different adaptations and genetic backgrounds, selection should favour the closing of species boundaries and zero gene flow, a process known as reinforcement. Recently, numerous cases of gene flow between species have been identified, many of which involved adaptive introgression of beneficial alleles. These cases could reflect transient states on the way to closed species boundaries or the result of declining strength or efficacy of selection for reinforcement as the level of gene flow approaches zero. An alternative hypothesis, however, is that selection favours porous species boundaries that allow beneficial alleles to cross, especially in changing environments. This perspective evaluates the conditions that would be needed for selection to favour porous species boundaries and the evidence for them. A contrast is made between hybridization in sexual eukaryotes and gene transfer via homologous recombination in bacteria. Current evidence is inconclusive on whether non-zero gene flow is favoured by selection. Studies are needed that quantify selection gradients on rates of gene flow and test for evolution towards intermediate values, especially experiments that manipulate conditions and track evolution for multiple generations. Estimation of gene flow networks for more clades and regional assemblages using emerging genome data will also allow the evolutionary determinants of interspecific gene flow to be better understood.
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6
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Dalui S, Sharma LK, Thakur M. Barriers and corridors: Assessment of gene flow and movement among red panda populations in eastern Himalayas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172523. [PMID: 38657804 DOI: 10.1016/j.scitotenv.2024.172523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/14/2024] [Accepted: 04/14/2024] [Indexed: 04/26/2024]
Abstract
Landscape features can impede dispersal, gene flow, and population demography, resulting in the formation of several meta-populations within a continuous landscape. Understanding a species' ability to overcome these barriers is critical for predicting genetic connectivity and population persistence, and implementing effective conservation strategies. In the present study, we conducted a fine-scale spatial genetic analysis to understand the contemporary gene flow within red panda populations in the Eastern Himalayas. Employing geometric aspects of reserve design, we delineated the critical core habitats for red pandas, which comprise 14.5 % of the landscape (12,189.75 Km2), with only a mere 443 Km2 falling within the protected areas. We identified corridors among the core habitats, which may be vital for the species' long-term genetic viability. Furthermore, we identified substantial landscape barriers, including Sela Pass in the western region, Siang river in the central region, and the Dibang river, Lohit river, along with Dihang, Dipher, and Kumjawng passes in the eastern region, which hinder gene flow. We suggest managing red panda populations through the creation of Community Conservation Reserves in the identified core habitats, following landscape-level management planning based on the core principles of geometric reserve design. This includes a specific emphasis on identified core habitats of red panda (CH-RP 5 and CH-RP 8) to facilitate corridors and implement meta-population dynamics. We propose the development of a comprehensive, long-term conservation and management plan for red pandas in the transboundary landscape, covering China, Nepal, and Bhutan.
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Affiliation(s)
- Supriyo Dalui
- Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053, India; Department of Zoology, University of Calcutta, Kolkata, West Bengal 700019, India
| | - Lalit Kumar Sharma
- Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053, India
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053, India.
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7
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Touchette L, Godbout J, Lamothe M, Porth I, Isabel N. A cryptic syngameon within Betula shrubs revealed: Implications for conservation in changing subarctic environments. Evol Appl 2024; 17:e13689. [PMID: 38633131 PMCID: PMC11022622 DOI: 10.1111/eva.13689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 02/06/2024] [Accepted: 03/20/2024] [Indexed: 04/19/2024] Open
Abstract
Arctic and subarctic ecosystems are rapidly transforming due to global warming, emphasizing the need to understand the genetic diversity and adaptive strategies of northern plant species for effective conservation. This study focuses on Betula glandulosa, a native North American tundra shrub known as dwarf birch, which demonstrates an apparent capacity to adapt to changing climate conditions. To address the taxonomic challenges associated with shrub birches and logistical complexities of sampling in the northernmost areas where species' ranges overlap, we adopted a multicriteria approach. Incorporating molecular data, ploidy level assessment and leaf morphology, we aimed to distinguish B. glandulosa individuals from other shrub birch species sampled. Our results revealed three distinct species and their hybrids within the 537 collected samples, suggesting the existence of a shrub birch syngameon, a reproductive network of interconnected species. Additionally, we identified two discrete genetic clusters within the core species, B. glandulosa, that likely correspond to two different glacial lineages. A comparison between the nuclear and chloroplast SNP data emphasizes a long history of gene exchange between different birch species and genetic clusters. Furthermore, our results highlight the significance of incorporating interfertile congeneric species in conservation strategies and underscores the need for a holistic approach to conservation in the context of climate change, considering the complex dynamics of species interactions. While further research will be needed to describe this shrub birches syngameon and its constituents, this study is a first step in recognizing its existence and disseminating awareness among ecologists and conservation practitioners. This biological phenomenon, which offers evolutionary flexibility and resilience beyond what its constituent species can achieve individually, may have significant ecological implications.
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Affiliation(s)
- Lyne Touchette
- Department of Wood and Forest SciencesUniversité LavalQuebecQuebecCanada
- Natural Resources Canada, Canadian Forest ServiceLaurentian Forestry CentreQuebecQuebecCanada
- Centre for Forest ResearchUniversité LavalQuebecQuebecCanada
| | - Julie Godbout
- Ministère des Ressources naturelles et des Forêts, Direction de la recherche forestièreQuébecQuébecCanada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest ServiceLaurentian Forestry CentreQuebecQuebecCanada
| | - Ilga Porth
- Department of Wood and Forest SciencesUniversité LavalQuebecQuebecCanada
- Centre for Forest ResearchUniversité LavalQuebecQuebecCanada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest ServiceLaurentian Forestry CentreQuebecQuebecCanada
- Centre for Forest ResearchUniversité LavalQuebecQuebecCanada
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Ravikanthachari N, Steward RA, Boggs CL. Patterns of genetic variation and local adaptation of a native herbivore to a lethal invasive plant. Mol Ecol 2024:e17326. [PMID: 38515231 DOI: 10.1111/mec.17326] [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: 06/08/2023] [Revised: 12/03/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024]
Abstract
Understanding the evolutionary processes that influence fitness is critical to predicting species' responses to selection. Interactions among evolutionary processes including gene flow, drift and the strength of selection can lead to either local adaptation or maladaptation, especially in heterogenous landscapes. Populations experiencing novel environments or resources are ideal for understanding the mechanisms underlying adaptation or maladaptation, specifically in locally co-evolved interactions. We used the interaction between a native herbivore that oviposits on a patchily distributed introduced plant that in turn causes significant mortality to the larvae to test for signatures of local adaptation in areas where the two co-occurred. We used whole-genome sequencing to explore population structure, patterns of gene flow and signatures of local adaptation. We found signatures of local adaptation in response to the introduced plant in the absence of strong population structure with no genetic differentiation and low genetic variation. Additionally, we found localized allele frequency differences within a single population between habitats with and without the lethal plant, highlighting the effects of strong selection. Finally, we identified that selection was acting on larval ability to feed on the plant rather than on females' ability to avoid oviposition, thus uncovering the specific ontogenetic target of selection. Our work highlights the potential for adaptation to occur in a fine-grained landscape in the presence of gene flow and low genetic variation.
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Affiliation(s)
- Nitin Ravikanthachari
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA
| | - Rachel A Steward
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA
- Department of Biology, Lund University, Lund, Sweden
| | - Carol L Boggs
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA
- School of Earth, Ocean & Environment, University of South Carolina, Columbia, South Carolina, USA
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9
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Dickel L, Arcese P, Keller LF, Nietlisbach P, Goedert D, Jensen H, Reid JM. Multigenerational Fitness Effects of Natural Immigration Indicate Strong Heterosis and Epistatic Breakdown in a Wild Bird Population. Am Nat 2024; 203:411-431. [PMID: 38358807 DOI: 10.1086/728669] [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: 02/17/2024]
Abstract
AbstractThe fitness of immigrants and their descendants produced within recipient populations fundamentally underpins the genetic and population dynamic consequences of immigration. Immigrants can in principle induce contrasting genetic effects on fitness across generations, reflecting multifaceted additive, dominance, and epistatic effects. Yet full multigenerational and sex-specific fitness effects of regular immigration have not been quantified within naturally structured systems, precluding inference on underlying genetic architectures and population outcomes. We used four decades of song sparrow (Melospiza melodia) life history and pedigree data to quantify fitness of natural immigrants, natives, and their F1, F2, and backcross descendants and test for evidence of nonadditive genetic effects. Values of key fitness components (including adult lifetime reproductive success and zygote survival) of F1 offspring of immigrant-native matings substantially exceeded their parent mean, indicating strong heterosis. Meanwhile, F2 offspring of F1-F1 matings had notably low values, indicating surprisingly strong epistatic breakdown. Furthermore, magnitudes of effects varied among fitness components and differed between female and male descendants. These results demonstrate that strong nonadditive genetic effects on fitness can arise within weakly structured and fragmented populations experiencing frequent natural immigration. Such effects will substantially affect the net degree of effective gene flow and resulting local genetic introgression and adaptation.
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10
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Terasaki Hart DE, Wang IJ. Genomic architecture controls multivariate adaptation to climate change. GLOBAL CHANGE BIOLOGY 2024; 30:e17179. [PMID: 38403891 DOI: 10.1111/gcb.17179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/11/2023] [Accepted: 01/12/2024] [Indexed: 02/27/2024]
Abstract
As climate change advances, environmental gradients may decouple, generating novel multivariate environments that stress wild populations. A commonly invoked mechanism of evolutionary rescue is adaptive gene flow tracking climate shifts, but gene flow from populations inhabiting similar conditions on one environmental axis could cause maladaptive introgression when populations are adapted to different environmental variables that do not shift together. Genomic architecture can play an important role in determining the effectiveness and relative magnitudes of adaptive gene flow and in situ adaptation. This may have direct consequences for how species respond to climate change but is often overlooked. Here, we simulated microevolutionary responses to environmental change under scenarios defined by variation in the polygenicity, linkage, and genetic redundancy of two independent traits, one of which is adapted to a gradient that shifts under climate change. We used these simulations to examine how genomic architecture influences evolutionary outcomes under climate change. We found that climate-tracking (up-gradient) gene flow, though present in all scenarios, was strongly constrained under scenarios of lower linkage and higher polygenicity and redundancy, suggesting in situ adaptation as the predominant mechanism of evolutionary rescue under these conditions. We also found that high polygenicity caused increased maladaptation and demographic decline, a concerning result given that many climate-adapted traits may be polygenic. Finally, in scenarios with high redundancy, we observed increased adaptive capacity. This finding adds to the growing recognition of the importance of redundancy in mediating in situ adaptive capacity and suggests opportunities for better understanding the climatic vulnerability of real populations.
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Affiliation(s)
- Drew E Terasaki Hart
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
- The Nature Conservancy, Arlington, Virginia, USA
- CSIRO Environment, Brisbane, Queensland, Australia
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
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11
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Feng X, Merilä J, Löytynoja A. Secondary Contact, Introgressive Hybridization, and Genome Stabilization in Sticklebacks. Mol Biol Evol 2024; 41:msae031. [PMID: 38366566 PMCID: PMC10903534 DOI: 10.1093/molbev/msae031] [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: 09/19/2023] [Revised: 12/20/2023] [Accepted: 02/09/2024] [Indexed: 02/18/2024] Open
Abstract
Advances in genomic studies have revealed that hybridization in nature is pervasive and raised questions about the dynamics of different genetic and evolutionary factors following the initial hybridization event. While recent research has proposed that the genomic outcomes of hybridization might be predictable to some extent, many uncertainties remain. With comprehensive whole-genome sequence data, we investigated the genetic introgression between 2 divergent lineages of 9-spined sticklebacks (Pungitius pungitius) in the Baltic Sea. We found that the intensity and direction of selection on the introgressed variation has varied across different genomic elements: while functionally important regions displayed reduced rates of introgression, promoter regions showed enrichment. Despite the general trend of negative selection, we identified specific genomic regions that were enriched for introgressed variants, and within these regions, we detected footprints of selection, indicating adaptive introgression. Geographically, we found the selection against the functional changes to be strongest in the vicinity of the secondary contact zone and weaken as a function of distance from the initial contact. Altogether, the results suggest that the stabilization of introgressed variation in the genomes is a complex, multistage process involving both negative and positive selection. In spite of the predominance of negative selection against introgressed variants, we also found evidence for adaptive introgression variants likely associated with adaptation to Baltic Sea environmental conditions.
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Affiliation(s)
- Xueyun Feng
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Juha Merilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
- Area of Ecology and Biodiversity, The School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
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12
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Clancey E, MacPherson A, Cheek RG, Mouton JC, Sillett TS, Ghalambor CK, Funk WC, Hohenlohe PA. Unraveling Adaptive Evolutionary Divergence at Microgeographic Scales. Am Nat 2024; 203:E35-E49. [PMID: 38306284 DOI: 10.1086/727723] [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: 02/04/2024]
Abstract
AbstractStriking examples of local adaptation at fine geographic scales are increasingly being documented in natural populations. However, the relative contributions made by natural selection, phenotype-dependent dispersal (when individuals disperse with respect to a habitat preference), and mate preference in generating and maintaining microgeographic adaptation and divergence are not well studied. Here, we develop quantitative genetics models and individual-based simulations (IBSs) to uncover the evolutionary forces that possibly drive microgeographic divergence. We also perform Bayesian estimation of the parameters in our IBS using empirical data on habitat-specific variation in bill morphology in the island scrub-jay (Aphelocoma insularis) to apply our models to a natural system. We find that natural selection and phenotype-dependent dispersal can generate the patterns of divergence we observe in the island scrub-jay. However, mate preference for a mate with similar bill morphology, even though observed in the species, does not play a significant role in driving divergence. Our modeling approach provides insights into phenotypic evolution occurring over small spatial scales relative to dispersal ranges, suggesting that adaptive divergence at microgeographic scales may be common across a wider range of taxa than previously thought. Our quantitative genetic models help to inform future theoretical and empirical work to determine how selection, habitat preference, and mate preference contribute to local adaptation and microgeographic divergence.
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13
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Goebl AM, Kane NC, Doak DF, Rieseberg LH, Ostevik KL. Adaptation to distinct habitats is maintained by contrasting selection at different life stages in sunflower ecotypes. Mol Ecol 2024; 33:e16785. [PMID: 36374153 DOI: 10.1111/mec.16785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/20/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
Conspecific populations living in adjacent but contrasting microenvironments represent excellent systems for studying natural selection. These systems are valuable because gene flow is expected to force genetic homogeneity except at loci experiencing divergent selection. A history of reciprocal transplant and common garden studies in such systems, and a growing number of genomic studies, have contributed to understanding how selection operates in natural populations. While selection can vary across different fitness components and life stages, few studies have investigated how this ultimately affects allele frequencies and the maintenance of divergence between populations. Here, we study two sunflower ecotypes in distinct, adjacent habitats by combining demographic models with genome-wide sequence data to estimate fitness and allele frequency change at multiple life stages. This framework allows us to estimate that only local ecotypes are likely to experience positive population growth (λ > 1) and that the maintenance of divergent adaptation appears to be mediated via habitat- and life stage-specific selection. We identify genetic variation, significantly driven by loci in chromosomal inversions, associated with different life history strategies in neighbouring ecotypes that optimize different fitness components and may contribute to the maintenance of distinct ecotypes.
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Affiliation(s)
- April M Goebl
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Daniel F Doak
- Environmental Studies Programme, University of Colorado, Boulder, Colorado, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kate L Ostevik
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Evolution, Ecology and Organismal Biology, University of California Riverside, Riverside, California, USA
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14
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Sun BJ, Li WM, Lv P, Wen GN, Wu DY, Tao SA, Liao ML, Yu CQ, Jiang ZW, Wang Y, Xie HX, Wang XF, Chen ZQ, Liu F, Du WG. Genetically Encoded Lizard Color Divergence for Camouflage and Thermoregulation. Mol Biol Evol 2024; 41:msae009. [PMID: 38243850 PMCID: PMC10835340 DOI: 10.1093/molbev/msae009] [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: 04/04/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/22/2024] Open
Abstract
Local adaptation is critical in speciation and evolution, yet comprehensive studies on proximate and ultimate causes of local adaptation are generally scarce. Here, we integrated field ecological experiments, genome sequencing, and genetic verification to demonstrate both driving forces and molecular mechanisms governing local adaptation of body coloration in a lizard from the Qinghai-Tibet Plateau. We found dark lizards from the cold meadow population had lower spectrum reflectance but higher melanin contents than light counterparts from the warm dune population. Additionally, the colorations of both dark and light lizards facilitated the camouflage and thermoregulation in their respective microhabitat simultaneously. More importantly, by genome resequencing analysis, we detected a novel mutation in Tyrp1 that underpinned this color adaptation. The allele frequencies at the site of SNP 459# in the gene of Tyrp1 are 22.22% G/C and 77.78% C/C in dark lizards and 100% G/G in light lizards. Model-predicted structure and catalytic activity showed that this mutation increased structure flexibility and catalytic activity in enzyme TYRP1, and thereby facilitated the generation of eumelanin in dark lizards. The function of the mutation in Tyrp1 was further verified by more melanin contents and darker coloration detected in the zebrafish injected with the genotype of Tyrp1 from dark lizards. Therefore, our study demonstrates that a novel mutation of a major melanin-generating gene underpins skin color variation co-selected by camouflage and thermoregulation in a lizard. The resulting strong selection may reinforce adaptive genetic divergence and enable the persistence of adjacent populations with distinct body coloration.
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Affiliation(s)
- Bao-Jun Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei-Ming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng Lv
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guan-Nan Wen
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dan-Yang Wu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shi-Ang Tao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming-Ling Liao
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Chang-Qing Yu
- Ecology Laboratory, Beijing Ecotech Science and Technology Ltd, Beijing 100190, China
| | - Zhong-Wen Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Wang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Hong-Xin Xie
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xi-Feng Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei-Guo Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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15
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Ravigné V, Rodrigues LR, Charlery de la Masselière M, Facon B, Kuczyński L, Radwan J, Skoracka A, Magalhães S. Understanding the joint evolution of dispersal and host specialisation using phytophagous arthropods as a model group. Biol Rev Camb Philos Soc 2024; 99:219-237. [PMID: 37724465 DOI: 10.1111/brv.13018] [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: 05/25/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Theory generally predicts that host specialisation and dispersal should evolve jointly. Indeed, many models predict that specialists should be poor dispersers to avoid landing on unsuitable hosts while generalists will have high dispersal abilities. Phytophagous arthropods are an excellent group to test this prediction, given extensive variation in their host range and dispersal abilities. Here, we explore the degree to which the empirical literature on this group is in accordance with theoretical predictions. We first briefly outline the theoretical reasons to expect such a correlation. We then report empirical studies that measured both dispersal and the degree of specialisation in phytophagous arthropods. We find a correlation between dispersal and levels of specialisation in some studies, but with wide variation in this result. We then review theoretical attributes of species and environment that may blur this correlation, namely environmental grain, temporal heterogeneity, habitat selection, genetic architecture, and coevolution between plants and herbivores. We argue that theoretical models fail to account for important aspects, such as phenotypic plasticity and the impact of selective forces stemming from other biotic interactions, on both dispersal and specialisation. Next, we review empirical caveats in the study of this interplay. We find that studies use different measures of both dispersal and specialisation, hampering comparisons. Moreover, several studies do not provide independent measures of these two traits. Finally, variation in these traits may occur at scales that are not being considered. We conclude that this correlation is likely not to be expected from large-scale comparative analyses as it is highly context dependent and should not be considered in isolation from the factors that modulate it, such as environmental scale and heterogeneity, intrinsic traits or biotic interactions. A stronger crosstalk between theoretical and empirical studies is needed to understand better the prevalence and basis of the correlation between dispersal and specialisation.
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Affiliation(s)
- Virginie Ravigné
- CIRAD, UMR PHIM, - PHIM, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, TA A-120/K, Campus international de Baillarguet, avenue du Campus d'Agropolis, Montpellier Cedex 5, 34398, France
| | - Leonor R Rodrigues
- cE3c: Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, edifício C2, Lisboa, 1749-016, Portugal
| | - Maud Charlery de la Masselière
- cE3c: Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, edifício C2, Lisboa, 1749-016, Portugal
| | - Benoît Facon
- CBGP, INRAE, IRD, CIRAD, Institut Agro, University of Montpellier, 755 avenue du Campus Agropolis, CS 34988, Montferrier sur Lez cedex, 30016, France
| | - Lechosław Kuczyński
- Population Ecology Lab, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Jacek Radwan
- Evolutionary Biology Group, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Anna Skoracka
- Population Ecology Lab, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Sara Magalhães
- cE3c: Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, edifício C2, Lisboa, 1749-016, Portugal
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16
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Meyer L, Barry P, Riquet F, Foote A, Der Sarkissian C, Cunha RL, Arbiol C, Cerqueira F, Desmarais E, Bordes A, Bierne N, Guinand B, Gagnaire PA. Divergence and gene flow history at two large chromosomal inversions underlying ecotype differentiation in the long-snouted seahorse. Mol Ecol 2024:e17277. [PMID: 38279695 DOI: 10.1111/mec.17277] [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: 06/20/2023] [Revised: 12/18/2023] [Accepted: 01/04/2024] [Indexed: 01/28/2024]
Abstract
Chromosomal inversions can play an important role in divergence and reproductive isolation by building and maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they can take the form of balanced polymorphisms that segregate within populations until one arrangement becomes fixed. Many questions remain about how inversion polymorphisms arise, how they are maintained over the long term, and ultimately, whether and how they contribute to speciation. The long-snouted seahorse (Hippocampus guttulatus) is genetically subdivided into geographic lineages and marine-lagoon ecotypes, with shared structural variation underlying lineage and ecotype divergence. Here, we aim to characterize structural variants and to reconstruct their history and suspected role in ecotype formation. We generated a near chromosome-level genome assembly and described genome-wide patterns of diversity and divergence through the analysis of 112 whole-genome sequences from Atlantic, Mediterranean, and Black Sea populations. By also analysing linked-read sequencing data, we found evidence for two chromosomal inversions that were several megabases in length and showed contrasting allele frequency patterns between lineages and ecotypes across the species range. We reveal that these inversions represent ancient intraspecific polymorphisms, one likely being maintained by divergent selection and the other by pseudo-overdominance. A possible selective coupling between the two inversions was further supported by the absence of specific haplotype combinations and a putative functional interaction between the two inversions in reproduction. Lastly, we detected gene flux eroding divergence between inverted alleles at varying levels for the two inversions, with a likely impact on their dynamics and contribution to divergence and speciation.
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Affiliation(s)
- Laura Meyer
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Pierre Barry
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto, Vairão, Portugal
| | | | - Andrew Foote
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Clio Der Sarkissian
- Centre for Anthropobiology and Genomics of Toulouse, CNRS, University of Toulouse Paul Sabatier, Toulouse, France
| | - Regina L Cunha
- Centre of Marine Sciences-CCMAR, University of Algarve, Faro, Portugal
| | | | | | - Erick Desmarais
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Anaïs Bordes
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Bruno Guinand
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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17
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Klein JD, Maduna SN, Dicken ML, da Silva C, Soekoe M, McCord ME, Potts WM, Hagen SB, Bester‐van der Merwe AE. Local adaptation with gene flow in a highly dispersive shark. Evol Appl 2024; 17:e13628. [PMID: 38283610 PMCID: PMC10810256 DOI: 10.1111/eva.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 01/30/2024] Open
Abstract
Adaptive divergence in response to environmental clines are expected to be common in species occupying heterogeneous environments. Despite numerous advances in techniques appropriate for non-model species, gene-environment association studies in elasmobranchs are still scarce. The bronze whaler or copper shark (Carcharhinus brachyurus) is a large coastal shark with a wide distribution and one of the most exploited elasmobranchs in southern Africa. Here, we assessed the distribution of neutral and adaptive genomic diversity in C. brachyurus across a highly heterogeneous environment in southern Africa based on genome-wide SNPs obtained through a restriction site-associated DNA method (3RAD). A combination of differentiation-based genome-scan (outflank) and genotype-environment analyses (redundancy analysis, latent factor mixed models) identified a total of 234 differentiation-based outlier and candidate SNPs associated with bioclimatic variables. Analysis of 26,299 putatively neutral SNPs revealed moderate and evenly distributed levels of genomic diversity across sites from the east coast of South Africa to Angola. Multivariate and clustering analyses demonstrated a high degree of gene flow with no significant population structuring among or within ocean basins. In contrast, the putatively adaptive SNPs demonstrated the presence of two clusters and deep divergence between Angola and all other individuals from Namibia and South Africa. These results provide evidence for adaptive divergence in response to a heterogeneous seascape in a large, mobile shark despite high levels of gene flow. These results are expected to inform management strategies and policy at the national and regional level for conservation of C. brachyurus populations.
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Affiliation(s)
- Juliana D. Klein
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
| | - Simo N. Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Matthew L. Dicken
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- Institute for Coastal and Marine Research (CMR), Ocean Sciences CampusNelson Mandela UniversityGqeberhaSouth Africa
| | - Charlene da Silva
- Department of Forestry, Fisheries and EnvironmentRogge BaySouth Africa
| | - Michelle Soekoe
- Division of Marine ScienceReel Science CoalitionCape TownSouth Africa
| | - Meaghen E. McCord
- South African Shark ConservancyHermanusSouth Africa
- Canadian Parks and Wilderness SocietyVancouverBritish ColumbiaCanada
| | - Warren M. Potts
- Department of Ichthyology and Fisheries ScienceRhodes UniversityMakhandaSouth Africa
- South African Institute for Aquatic BiodiversityMakhandaSouth Africa
| | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Aletta E. Bester‐van der Merwe
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
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18
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Hu LS, Dong YW. Multiple genetic sources facilitate the northward range expansion of an intertidal oyster along China's coast. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024; 34:e2764. [PMID: 36259430 DOI: 10.1002/eap.2764] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/27/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
Coastal artificial structures on the former mudflats provide available habitats for the rocky intertidal species which can establish new populations in these emerging habitats over their former distribution range limits. As a former southern species, the oyster Crassostrea sikamea has become a pioneer and rapidly invaded the artificial shorelines in northern China. We used a seascape genomics approach to investigate the population structure and genetic sources of C. sikamea on the coastal artificial structures, which is crucial for understanding the genetic mechanisms driving species distribution range expansion and invasion pathway of intertidal species. Five C. sikamea populations, including two artificial substrate populations (WGZ and ZAP), one oyster reef population (LS), and two natural rocky shore populations (ZS and XM), were measured using single nucleotide polymorphism (SNPs) obtained from double digest restriction-site associated DNA sequencing (ddRAD-Seq). Redundancy analyses (RDA) were implemented for investigating the relationship between local temperature variables and the temperature adaptability of C. sikamea. Genetic diversity, direction and strength of gene flow, and population structure all revealed that the LS and ZS populations were the genetic sources for the oyster populations on the emerging northern coastal artificial structures. Results of RDA showed that there were different adaptive potentials for northern and southern populations to local temperature variables and the oyster reef population which frequently suffers from heat stress owned high heat adaptability. The ZS population as a genetic source nearby the Yangtze River estuary provided mass larvae for the northern populations, and the other genetic source, the heat-tolerant LS population, in the oyster reef played an important role in the post-settlement success by providing preadapted genotypes. These results highlight the importance of multiple sources with divergent adaptative capabilities for biological invasion, and also emphasize the importance of the oyster reef in coastal biodiversity and conservation.
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Affiliation(s)
- Li-Sha Hu
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, People's Republic of China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
| | - Yun-Wei Dong
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, People's Republic of China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
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19
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Díaz-Arce N, Gagnaire PA, Richardson DE, Walter JF, Arnaud-Haond S, Fromentin JM, Brophy D, Lutcavage M, Addis P, Alemany F, Allman R, Deguara S, Fraile I, Goñi N, Hanke AR, Karakulak FS, Pacicco A, Quattro JM, Rooker JR, Arrizabalaga H, Rodríguez-Ezpeleta N. Unidirectional trans-Atlantic gene flow and a mixed spawning area shape the genetic connectivity of Atlantic bluefin tuna. Mol Ecol 2024; 33:e17188. [PMID: 37921120 DOI: 10.1111/mec.17188] [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: 06/21/2023] [Revised: 10/02/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023]
Abstract
The commercially important Atlantic bluefin tuna (Thunnus thynnus), a large migratory fish, has experienced notable recovery aided by accurate resource assessment and effective fisheries management efforts. Traditionally, this species has been perceived as consisting of eastern and western populations, spawning respectively in the Mediterranean Sea and the Gulf of Mexico, with mixing occurring throughout the Atlantic. However, recent studies have challenged this assumption by revealing weak genetic differentiation and identifying a previously unknown spawning ground in the Slope Sea used by Atlantic bluefin tuna of uncertain origin. To further understand the current and past population structure and connectivity of Atlantic bluefin tuna, we have assembled a unique dataset including thousands of genome-wide single-nucleotide polymorphisms (SNPs) from 500 larvae, young of the year and spawning adult samples covering the three spawning grounds and including individuals of other Thunnus species. Our analyses support two weakly differentiated but demographically connected ancestral populations that interbreed in the Slope Sea. Moreover, we also identified signatures of introgression from albacore (Thunnus alalunga) into the Atlantic bluefin tuna genome, exhibiting varied frequencies across spawning areas, indicating strong gene flow from the Mediterranean Sea towards the Slope Sea. We hypothesize that the observed genetic differentiation may be attributed to increased gene flow caused by a recent intensification of westward migration by the eastern population, which could have implications for the genetic diversity and conservation of western populations. Future conservation efforts should consider these findings to address potential genetic homogenization in the species.
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Affiliation(s)
- Natalia Díaz-Arce
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | | | - David E Richardson
- Northeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA), Narragansett, Rhode Island, USA
| | - John F Walter
- Southeast Fisheries Sciences Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA), Miami, Florida, USA
| | | | | | - Deirdre Brophy
- Marine and Freshwater Research Center, Atlantic Technological University (ATU), Galway City, Ireland
| | - Molly Lutcavage
- Large Pelagics Research Center, School for the Environment, University of Massachusetts Boston, Gloucester, Massachusetts, USA
| | - Piero Addis
- Department of Environmental and Life Science, University of Cagliari, Cagliari, Italy
| | - Francisco Alemany
- International Commission for the Conservation of Atlantic Tunas, GBYP, Madrid, Spain
| | - Robert Allman
- National Marine Fisheries Service, Southeast Fisheries Science Center, Panama City Laboratory, Panama City, Florida, USA
| | | | - Igaratza Fraile
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Spain
| | - Nicolas Goñi
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Spain
| | - Alex R Hanke
- St Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, New Brunswick, Canada
| | | | - Ashley Pacicco
- Cooperative Institute for Marine and Atmospheric Studies Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, Florida, USA
| | - Joseph M Quattro
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| | - Jay R Rooker
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, Texas, USA
| | - Haritz Arrizabalaga
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Spain
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20
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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.
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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.
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21
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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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22
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Petak C, Frati L, Brennan RS, Pespeni MH. Whole-Genome Sequencing Reveals That Regulatory and Low Pleiotropy Variants Underlie Local Adaptation to Environmental Variability in Purple Sea Urchins. Am Nat 2023; 202:571-586. [PMID: 37792925 DOI: 10.1086/726013] [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: 10/06/2023]
Abstract
AbstractOrganisms experience environments that vary across both space and time. Such environmental heterogeneity shapes standing genetic variation and may influence species' capacity to adapt to rapid environmental change. However, we know little about the kind of genetic variation that is involved in local adaptation to environmental variability. To address this gap, we sequenced the whole genomes of 140 purple sea urchins (Strongylocentrotus purpuratus) from seven populations that vary in their degree of pH variability. Despite no evidence of global population structure, we found a suite of single-nucleotide polymorphisms (SNPs) tightly correlated with local pH variability (outlier SNPs), which were overrepresented in regions putatively involved in gene regulation (long noncoding RNA and enhancers), supporting the idea that variation in regulatory regions is important for local adaptation to variability. In addition, outliers in genes were found to be (i) enriched for biomineralization and ion homeostasis functions related to low pH response, (ii) less central to the protein-protein interaction network, and (iii) underrepresented among genes highly expressed during early development. Taken together, these results suggest that loci that underlie local adaptation to pH variability in purple sea urchins fall in regions with potentially low pleiotropic effects (based on analyses involving regulatory regions, network centrality, and expression time) involved in low pH response (based on functional enrichment).
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23
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Faria AVF, Martins NT, Ayres-Ostrock LM, Gurgel CFD, Plastino EM. Phylogeography of the red alga Gracilariopsis tenuifrons (Gracilariales) along the Brazilian coast. JOURNAL OF PHYCOLOGY 2023; 59:1041-1052. [PMID: 37435655 DOI: 10.1111/jpy.13363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/01/2023] [Accepted: 06/15/2023] [Indexed: 07/13/2023]
Abstract
Changes in the sea level during the Holocene are regarded as one of the most prevalent drivers of the diversity and distribution of macroalgae in Brazil, influenced by the emergence of the Vitória-Trindade seamount chain (VTC). Gracilariopsis tenuifrons has a wide geographic distribution along the Brazilian coast, from Maranhão state (2°48'64.3" S) to Santa Catarina state (27.5°73'83" S). The knowledge of historical processes affecting diversity may allow the development of conservation strategies in environments against anthropogenic influence. Therefore, knowledge about phylogeography and populational genetic diversity in G. tenuifrons is necessary. Six populations were sampled along the northeastern tropical (Maranhão-MA, Rio Grande do Norte-RN, Alagoas-AL, and Bahia-BA States) and southeastern subtropical (São Paulo "Ubatuba"-SP1 and São Paulo "Itanhaém"-SP2 States) regions along the Brazilian coast. The genetic diversity and structure of G. tenuifrons were inferred using mitochondrial (COI-5P and cox2-3 concatenated) DNA markers. Gracilariopsis tenuifrons populations showed an evident separation between the northeast (from 2°48'64.3" S to 14°18'23" S; 17 haplotypes) and the southeast (from 23°50'14.9" S to 24°20'04.7" S; 10 haplotypes) regions by two mutational steps between them. The main biogeographical barrier to gene flow is located nearby the VTC. The southeast region (São Paulo State) is separated by two subphylogroups (SP1, three haplotypes and SP2, six haplotypes), and Santos Bay (estuary) has been considered a biogeographical barrier between them. The presence of genetic structure and putative barriers to gene flow are in concordance with previous studies reporting biogeographic breaks in the southwest Atlantic Ocean, including the genetic isolation between northeast and southeast regions for red and brown algae in the vicinity of the VTC.
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Affiliation(s)
- Andre V F Faria
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Nuno T Martins
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Ligia M Ayres-Ostrock
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Hortimare-Breeding and Propagating Seaweed, Heerhugowaard, The Netherlands
| | - Carlos F D Gurgel
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Estela M Plastino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Maduna SN, Jónsdóttir ÓDB, Imsland AKD, Gíslason D, Reynolds P, Kapari L, Hangstad TA, Meier K, Hagen SB. Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish-Implications for Broodstock Provenance Sourcing and Larval Production. Genes (Basel) 2023; 14:1870. [PMID: 37895225 PMCID: PMC10606024 DOI: 10.3390/genes14101870] [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: 08/21/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Aquaculture of the lumpfish (Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for "cleaner fish" to minimise sea lice infestations in Atlantic salmon mariculture farms. We used over 10K genome-wide single nucleotide polymorphisms (SNPs) to investigate the spatial patterns of genomic variation in the lumpfish along the coast of Norway and across the North Atlantic. Moreover, we applied three genome scans for outliers and two genotype-environment association tests to assess the signatures and patterns of local adaptation under extensive gene flow. With our 'global' sampling regime, we found two major genetic groups of lumpfish, i.e., the western and eastern Atlantic. Regionally in Norway, we found marginal evidence of population structure, where the population genomic analysis revealed a small portion of individuals with a different genetic ancestry. Nevertheless, we found strong support for local adaption under high gene flow in the Norwegian lumpfish and identified over 380 high-confidence environment-associated loci linked to gene sets with a key role in biological processes associated with environmental pressures and embryonic development. Our results bridge population genetic/genomics studies with seascape genomics studies and will facilitate genome-enabled monitoring of the genetic impacts of escapees and allow for genetic-informed broodstock selection and management in Norway.
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Affiliation(s)
- Simo Njabulo Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway;
| | | | - Albert Kjartan Dagbjartarson Imsland
- Akvaplan-Niva Iceland Office, Akralind 6, 201 Kópavogur, Iceland; (Ó.D.B.J.); (A.K.D.I.)
- Department of Biological Sciences, High Technology Centre, University of Bergen, 5020 Bergen, Norway
| | | | | | - Lauri Kapari
- Akvaplan-Niva, Framsenteret, 9296 Tromsø, Norway;
| | | | | | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway;
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Euclide PT, Larson WA, Shi Y, Gruenthal K, Christensen KA, Seeb J, Seeb L. Conserved islands of divergence associated with adaptive variation in sockeye salmon are maintained by multiple mechanisms. Mol Ecol 2023. [PMID: 37695544 DOI: 10.1111/mec.17126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
Local adaptation is facilitated by loci clustered in relatively few regions of the genome, termed genomic islands of divergence. The mechanisms that create and maintain these islands and how they contribute to adaptive divergence is an active research topic. Here, we use sockeye salmon as a model to investigate both the mechanisms responsible for creating islands of divergence and the patterns of differentiation at these islands. Previous research suggested that multiple islands contributed to adaptive radiation of sockeye salmon. However, the low-density genomic methods used by these studies made it difficult to fully elucidate the mechanisms responsible for islands and connect genotypes to adaptive variation. We used whole genome resequencing to genotype millions of loci to investigate patterns of genetic variation at islands and the mechanisms that potentially created them. We discovered 64 islands, including 16 clustered in four genomic regions shared between two isolated populations. Characterisation of these four regions suggested that three were likely created by structural variation, while one was created by processes not involving structural variation. All four regions were small (< 600 kb), suggesting low recombination regions do not have to span megabases to be important for adaptive divergence. Differentiation at islands was not consistently associated with established population attributes. In sum, the landscape of adaptive divergence and the mechanisms that create it are complex; this complexity likely helps to facilitate fine-scale local adaptation unique to each population.
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Affiliation(s)
- Peter T Euclide
- Department of Forestry and Natural Resources, Illinois-Indiana Sea Grant, Purdue University, West Lafayette, Indiana, USA
| | - Wesley A Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science Center, Auke Bay Laboratories, Juneau, Alaska, USA
| | - Yue Shi
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Juneau, Alaska, USA
| | - Kristen Gruenthal
- Alaska Department of Fish and Game, Juneau, Alaska, USA
- Office of Applied Science, Wisconsin Department of Natural Resources, Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, Wisconsin, USA
| | - Kris A Christensen
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Jim Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Lisa Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
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Gonçalves-Dias J, Singh A, Graf C, Stetter MG. Genetic Incompatibilities and Evolutionary Rescue by Wild Relatives Shaped Grain Amaranth Domestication. Mol Biol Evol 2023; 40:msad177. [PMID: 37552934 PMCID: PMC10439364 DOI: 10.1093/molbev/msad177] [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: 04/25/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
Crop domestication and the subsequent expansion of crops have long been thought of as a linear process from a wild ancestor to a domesticate. However, evidence of gene flow from locally adapted wild relatives that provided adaptive alleles into crops has been identified in multiple species. Yet, little is known about the evolutionary consequences of gene flow during domestication and the interaction of gene flow and genetic load in crop populations. We study the pseudo-cereal grain amaranth that has been domesticated three times in different geographic regions of the Americas. We quantify the amount and distribution of gene flow and genetic load along the genome of the three grain amaranth species and their two wild relatives. Our results show ample gene flow between crop species and between crops and their wild relatives. Gene flow from wild relatives decreased genetic load in the three crop species. This suggests that wild relatives could provide evolutionary rescue by replacing deleterious alleles in crops. We assess experimental hybrids between the three crop species and found genetic incompatibilities between one Central American grain amaranth and the other two crop species. These incompatibilities might have created recent reproductive barriers and maintained species integrity today. Together, our results show that gene flow played an important role in the domestication and expansion of grain amaranth, despite genetic species barriers. The domestication of plants was likely not linear and created a genomic mosaic by multiple contributors with varying fitness effects for today's crops.
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Affiliation(s)
| | - Akanksha Singh
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Corbinian Graf
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Markus G Stetter
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
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27
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Snead AA, Tatarenkov A, Avise JC, Taylor DS, Turner BJ, Marson K, Earley RL. Out to sea: ocean currents and patterns of asymmetric gene flow in an intertidal fish species. Front Genet 2023; 14:1206543. [PMID: 37456662 PMCID: PMC10349204 DOI: 10.3389/fgene.2023.1206543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Passive dispersal via wind or ocean currents can drive asymmetric gene flow, which influences patterns of genetic variation and the capacity of populations to evolve in response to environmental change. The mangrove rivulus fish (Kryptolebias marmoratus), hereafter "rivulus," is an intertidal fish species restricted to the highly fragmented New World mangrove forests of Central America, the Caribbean, the Bahamas, and Florida. Mangrove patches are biological islands with dramatic differences in both abiotic and biotic conditions compared to adjacent habitat. Over 1,000 individual rivulus across 17 populations throughout its range were genotyped at 32 highly polymorphic microsatellites. Range-wide population genetic structure was evaluated with five complementary approaches that found eight distinct population clusters. However, an analysis of molecular variance indicated significant population genetic structure among regions, populations within regions, sampling locations within populations, and individuals within sampling locations, indicating that rivulus has both broad- and fine-scale genetic differentiation. Integrating range-wide genetic data with biophysical modeling based on 10 years of ocean current data showed that ocean currents and the distance between populations over water drive gene flow patterns on broad scales. Directional migration estimates suggested some significant asymmetries in gene flow that also were mediated by ocean currents and distance. Specifically, populations in the center of the range (Florida Keys) were identified as sinks that received migrants (and alleles) from other populations but failed to export individuals. These populations thus harbor genetic variation, perhaps even from extirpated populations across the range, but ocean currents and complex arrangements of landmasses might prevent the distribution of that genetic variation elsewhere. Hence, the inherent asymmetry of ocean currents shown to impact both genetic differentiation and directional migration rates may be responsible for the complex distribution of genetic variation across the range and observed patterns of metapopulation structure.
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Affiliation(s)
- Anthony A. Snead
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Andrey Tatarenkov
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
| | - John C. Avise
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
| | | | - Bruce J. Turner
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Kristine Marson
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Ryan L. Earley
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
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Mittermayer F, Helmerson C, Duvetorp M, Johannesson K, Panova M. The molecular background of the aspartate aminotransferase polymorphism in Littorina snails maintained by strong selection on small spatial scales. Gene 2023:147517. [PMID: 37257792 DOI: 10.1016/j.gene.2023.147517] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/14/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
Allozymes present several classical examples of divergent selection, including the variation in the cytosolic aspartate aminotransferase (AAT) in the intertidal snails Littorina saxatilis. AAT is a part of the asparate-malate shuttle, in the interidal molluscs involved in the anaerobic respiration during desiccation. Previous allozyme studies reported the sharp gradient in the frequencies of the AAT100and the AAT120 alleles between the low and high shores in the Northern Europe and the differences in their enzymatic activity, supporting the role of AAT in adaptation to desiccation. However, the populations in the Iberian Peninsula showed the opposite allele cline. Using the mRNA sequencing and the genome pool-seq analyses we characterize DNA sequences of the different AAT alleles, report the amino acid replacements behind the allozyme variation and show that same allozyme alleles in Northern and Southern populations have different protein sequences. Gene phylogeny reveals that the AAT100 and the northern AAT120 alleles represent the old polymorphism, shared among the closely related species of Littorina, while the southern AAT120 allele is more recently derived from AAT100. Further, we show that the Aat gene is expressed at constitutive level in different genotypes and conditions, supporting the role of structural variation in regulation of enzyme activity. Finally, we report the location and the structure of the gene in the L. saxatilis genome and the presence of two additional non-functional gene copies. Altogether, we provide a missing link between the classical allozyme studies and the genome scans and bring together the results produced over decades of the genetic research.
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Affiliation(s)
- Felix Mittermayer
- Research Division Marine Ecology, Research Unit Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany; Department of Marine Sciences, University of Gothenburg, Tjärnö, 45296 Strömstad, Sweden
| | - Cecilia Helmerson
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo; Department of Marine Sciences, University of Gothenburg, Tjärnö, 45296 Strömstad, Sweden
| | - Mårten Duvetorp
- Department of Marine Sciences, University of Gothenburg, Tjärnö, 45296 Strömstad, Sweden
| | - Kerstin Johannesson
- Department of Marine Sciences, University of Gothenburg, Tjärnö, 45296 Strömstad, Sweden
| | - Marina Panova
- Department of Marine Sciences, University of Gothenburg, Tjärnö, 45296 Strömstad, Sweden.
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29
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van Mantgem PJ, Milano ER, Dudney J, Nesmith JCB, Vandergast AG, Zald HSJ. Growth, drought response, and climate-associated genomic structure in whitebark pine in the Sierra Nevada of California. Ecol Evol 2023; 13:e10072. [PMID: 37206686 PMCID: PMC10191741 DOI: 10.1002/ece3.10072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/21/2023] Open
Abstract
Whitebark pine (Pinus albicaulis Engelm.) has experienced rapid population declines and is listed as threatened under the Endangered Species Act in the United States. Whitebark pine in the Sierra Nevada of California represents the southernmost end of the species' distribution and, like other portions of its range, faces threats from an introduced pathogen, native bark beetles, and a rapidly warming climate. Beyond these chronic stressors, there is also concern about how this species will respond to acute stressors, such as drought. We present patterns of stem growth from 766 large (average diameter at breast height >25 cm), disease-free whitebark pine across the Sierra Nevada before and during a recent period of drought. We contextualize growth patterns using population genomic diversity and structure from a subset of 327 trees. Sampled whitebark pine generally had positive to neutral stem growth trends from 1970 to 2011, which was positively correlated with minimum temperature and precipitation. Indices of stem growth during drought years (2012 to 2015) relative to a predrought interval were mostly positive to neutral at our sampled sites. Individual tree growth response phenotypes appeared to be linked to genotypic variation in climate-associated loci, suggesting that some genotypes can take better advantage of local climatic conditions than others. We speculate that reduced snowpack during the 2012 to 2015 drought years may have lengthened the growing season while retaining sufficient moisture to maintain growth at most study sites. Growth responses may differ under future warming, however, particularly if drought severity increases and modifies interactions with pests and pathogens.
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Affiliation(s)
| | - Elizabeth R. Milano
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
- Present address:
USDA Forest ServiceRocky Mountain Research StationMoscowIdahoUSA
| | - Joan Dudney
- Environmental Studies ProgramUC Santa BarbaraSanta BarbaraCaliforniaUSA
- Department of Environmental Science, Policy, & ManagementUC BerkeleyBerkeleyCaliforniaUSA
- Department of Plant SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | | | - Amy G. Vandergast
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
| | - Harold S. J. Zald
- USDA Forest ServicePacific Northwest Research StationCorvallisOregonUSA
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30
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Ceccobelli S, Landi V, Senczuk G, Mastrangelo S, Sardina MT, Ben-Jemaa S, Persichilli C, Karsli T, Bâlteanu VA, Raschia MA, Poli MA, Ciappesoni G, Muchadeyi FC, Dzomba EF, Kunene NW, Lühken G, Deniskova TE, Dotsev AV, Zinovieva NA, Zsolnai A, Anton I, Kusza S, Carolino N, Santos-Silva F, Kawęcka A, Świątek M, Niżnikowski R, Špehar M, Anaya G, Granero A, Perloiro T, Cardoso P, Grande S, de Los Santos BL, Danchin-Burge C, Pasquini M, Martínez Martínez A, Delgado Bermejo JV, Lasagna E, Ciani E, Sarti FM, Pilla F. A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds. Genet Sel Evol 2023; 55:24. [PMID: 37013467 PMCID: PMC10069132 DOI: 10.1186/s12711-023-00797-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations), XP-EHH (cross-population extended haplotype homozygosity), and runs of homozygosity (ROH) islands were applied to identify genomic variants with potential impact on the adaptability of Merino genetic type in two contrasting climate zones. RESULTS The results indicate that a large part of the Merino's genetic relatedness and admixture patterns are explained by their genetic background and/or geographic origin, followed by local admixture. Multi-dimensional scaling, Neighbor-Net, Admixture, and TREEMIX analyses consistently provided evidence of the role of Australian, Rambouillet and German strains in the extensive gene introgression into the other Merino and Merino-derived breeds. The close relationship between Iberian Merinos and other South-western European breeds is consistent with the Iberian origin of the Merino genetic type, with traces from previous contributions of other Mediterranean stocks. Using Rsb and XP-EHH approaches, signatures of selection were detected spanning four genomic regions located on Ovis aries chromosomes (OAR) 1, 6 and 16, whereas two genomic regions on OAR6, that partially overlapped with the previous ones, were highlighted by ROH islands. Overall, the three approaches identified 106 candidate genes putatively under selection. Among them, genes related to immune response were identified via the gene interaction network. In addition, several candidate genes were found, such as LEKR1, LCORL, GHR, RBPJ, BMPR1B, PPARGC1A, and PRKAA1, related to morphological, growth and reproductive traits, adaptive thermogenesis, and hypoxia responses. CONCLUSIONS To the best of our knowledge, this is the first comprehensive dataset that includes most of the Merino and Merino-derived sheep breeds raised in different regions of the world. The results provide an in-depth picture of the genetic makeup of the current Merino and Merino-derived breeds, highlighting the possible selection pressures associated with the combined effect of anthropic and environmental factors. The study underlines the importance of Merino genetic types as invaluable resources of possible adaptive diversity in the context of the occurring climate changes.
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Affiliation(s)
- Simone Ceccobelli
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, 60131, Ancona, Italy.
| | - Vincenzo Landi
- Department of Veterinary Medicine, University of Bari ''Aldo Moro", 70010, Valenzano, Italy
| | - Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | - Maria Teresa Sardina
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | - Slim Ben-Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, 2049, Ariana, Tunisia
| | - Christian Persichilli
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Taki Karsli
- Department of Animal Science, Faculty of Agriculture, Eskisehir Osmangazi University, 26040, Eskisehir, Turkey
| | - Valentin-Adrian Bâlteanu
- Laboratory of Genomics, Biodiversity, Animal Breeding and Molecular Pathology, Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, 400372, Cluj-Napoca, Romania
| | - María Agustina Raschia
- Instituto de Genética "Ewald A. Favret", Instituto Nacional de Tecnología Agropecuaria, CICVyA-CNIA, B1686, Hurlingham, Buenos Aires, Argentina
| | - Mario Andrés Poli
- Instituto de Genética "Ewald A. Favret", Instituto Nacional de Tecnología Agropecuaria, CICVyA-CNIA, B1686, Hurlingham, Buenos Aires, Argentina
| | - Gabriel Ciappesoni
- Instituto Nacional de Investigación Agropecuaria, 90200, Canelones, Uruguay
| | | | - Edgar Farai Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, 3209, Scottsville, Pietermaritzburg, South Africa
| | | | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University, 35390, Giessen, Germany
| | | | | | | | - Attila Zsolnai
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, 2053, Herceghalom, Hungary
| | - István Anton
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, 2053, Herceghalom, Hungary
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032, Debrecen, Hungary
| | - Nuno Carolino
- Instituto Nacional de Investigação Agrária e Veterinária, 2005-048, Vale de Santarém, Portugal
| | - Fátima Santos-Silva
- Instituto Nacional de Investigação Agrária e Veterinária, 2005-048, Vale de Santarém, Portugal
| | - Aldona Kawęcka
- Department of Sheep and Goat Breeding, National Research Institute of Animal Production, 32-083, Kraków, Poland
| | - Marcin Świątek
- Department of Animal Breeding, Institute of Animal Sciences, Warsaw University of Life Sciences-SGGW, 02-786, Warsaw, Poland
| | - Roman Niżnikowski
- Department of Animal Breeding, Institute of Animal Sciences, Warsaw University of Life Sciences-SGGW, 02-786, Warsaw, Poland
| | - Marija Špehar
- Croatian Agency for Agriculture and Food, 10000, Zagreb, Croatia
| | - Gabriel Anaya
- MERAGEM Group, Department of Genetics, University of Córdoba, 14071, Córdoba, Spain
| | - Antonio Granero
- Asociación Nacional de Criadores de Ganado Merino (ACME), 28028, Madrid, Spain
| | - Tiago Perloiro
- Associação Nacional de Criadores de Ovinos da Raça Merina (ANCORME), 7005-665, Évora, Portugal
| | - Pedro Cardoso
- Associação de Produtores Agropecuários (OVIBEIRA), 6000-244, Castelo Branco, Portugal
| | - Silverio Grande
- Associazione Nazionale della Pastorizia (ASSONAPA), 00187, Rome, Italy
| | | | | | - Marina Pasquini
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, 60131, Ancona, Italy
| | | | | | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Elena Ciani
- Department of Bioscience, Biotechnology and Biopharmaceutics, University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Fabio Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
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Jiménez-Ramírez A, Solé-Medina A, Ramírez-Valiente JA, Robledo-Arnuncio JJ. Microgeographic variation in early fitness traits of Pinus sylvestris from contrasting soils. AMERICAN JOURNAL OF BOTANY 2023; 110:e16159. [PMID: 36943007 DOI: 10.1002/ajb2.16159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 05/11/2023]
Abstract
PREMISE The possibility of fine-scale intraspecific adaptive divergence under gene flow is established by theoretical models and has been confirmed empirically in tree populations distributed along steep altitudinal clines or across extreme edaphic discontinuities. However, the possibility of microgeographic adaptive divergence due to less severe but more frequent kinds of soil variation is unclear. METHODS In this study, we looked for evidence of local adaptation to calcareous versus siliceous soil types in two nearby Mediterranean Pinus sylvestris populations connected via pollen flow. Using a greenhouse experiment, we tested for variation in early (up to three years of age) seedling performance among open-pollinated maternal families originating from each edaphic provenance when experimentally grown on both types of natural local substrate. RESULTS Although seedlings were clearly affected by the edaphic environment, exhibiting lower and slower emergence as well as higher mortality on the calcareous than in the siliceous substrate, neither the performance on each substrate nor the plasticity among substrates varied significantly with seedling edaphic provenance. CONCLUSIONS We found no evidence of local adaptation to a non-extreme edaphic discontinuity over a small spatial scale, at least during early stages of seedling establishment. Future studies on microgeographic soil-driven adaptation should consider long-term experiments to minimize maternal effects and allow a potentially delayed expression of edaphic adaptive divergence.
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Affiliation(s)
- Azucena Jiménez-Ramírez
- Instituto de Ciencias Forestales, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (ICIFOR-INIA), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Department of Genetics, Faculty of Biological Sciences, Complutense University of Madrid, Madrid, Spain
| | - Aida Solé-Medina
- Instituto de Ciencias Forestales, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (ICIFOR-INIA), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - José A Ramírez-Valiente
- Instituto de Ciencias Forestales, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (ICIFOR-INIA), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Ecological and Forestry Applications Research Centre (CREAF), Cerdanyola del Vallès, Spain
| | - Juan J Robledo-Arnuncio
- Instituto de Ciencias Forestales, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (ICIFOR-INIA), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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Warson J, Baguette M, Stevens VM, Honnay O, De Kort H. The impact of habitat loss on molecular signatures of coevolution between an iconic butterfly (Alcon blue) and its host plant (Marsh gentian). J Hered 2023; 114:22-34. [PMID: 36749638 DOI: 10.1093/jhered/esac059] [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: 03/23/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022] Open
Abstract
Habitat loss is threatening natural communities worldwide. Small and isolated populations suffer from inbreeding and genetic drift, which jeopardize their long-term survival and adaptive capacities. However, the consequences of habitat loss for reciprocal coevolutionary interactions remain poorly studied. In this study, we investigated the effects of decreasing habitat patch size and connectivity associated with habitat loss on molecular signatures of coevolution in the Alcon blue butterfly (Phengaris alcon) and its most limited host, the marsh gentian (Gentiana pneumonanthe). Because reciprocal coevolution is characterized by negative frequency-dependent selection as a particular type of balancing selection, we investigated how signatures of balancing selection vary along a gradient of patch size and connectivity, using single nucleotide polymorphisms (SNPs). We found that signatures of coevolution were unaffected by patch characteristics in the host plants. On the other hand, more pronounced signatures of coevolution were observed in both spatially isolated and in large Alcon populations, together with pronounced spatial variation in SNPs that are putatively involved in coevolution. These findings suggest that habitat loss can facilitate coevolution in large butterfly populations through limiting swamping of locally beneficial alleles by maladaptive ones. We also found that allelic richness (Ar) of the coevolutionary SNPs is decoupled from neutral Ar in the butterfly, indicating that habitat loss has different effects on coevolutionary as compared with neutral processes. We conclude that this specialized coevolutionary system requires particular conservation interventions aiming at generating a spatial mosaic of both connected and of isolated habitat to maintain coevolutionary dynamics.
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Affiliation(s)
- Jonas Warson
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Heverlee, Belgium
- Leuven Plant Institute, Heverlee, Belgium
| | - Michel Baguette
- Centre National de la Recherche Scientifique, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, Moulis, France
- Institut Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 Museum National d'HistoireNaturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Virginie M Stevens
- Centre National de la Recherche Scientifique, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, Moulis, France
| | - Olivier Honnay
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Heverlee, Belgium
- Leuven Plant Institute, Heverlee, Belgium
| | - Hanne De Kort
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Heverlee, Belgium
- Leuven Plant Institute, Heverlee, Belgium
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Torres E, García-Fernández A, Iñigo D, Lara-Romero C, Morente-López J, Prieto-Benítez S, Rubio Teso ML, Iriondo JM. Facilitated Adaptation as A Conservation Tool in the Present Climate Change Context: A Methodological Guide. PLANTS (BASEL, SWITZERLAND) 2023; 12:1258. [PMID: 36986946 PMCID: PMC10053585 DOI: 10.3390/plants12061258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Climate change poses a novel threat to biodiversity that urgently requires the development of adequate conservation strategies. Living organisms respond to environmental change by migrating to locations where their ecological niche is preserved or by adapting to the new environment. While the first response has been used to develop, discuss and implement the strategy of assisted migration, facilitated adaptation is only beginning to be considered as a potential approach. Here, we present a review of the conceptual framework for facilitated adaptation, integrating advances and methodologies from different disciplines. Briefly, facilitated adaptation involves a population reinforcement that introduces beneficial alleles to enable the evolutionary adaptation of a focal population to pressing environmental conditions. To this purpose, we propose two methodological approaches. The first one (called pre-existing adaptation approach) is based on using pre-adapted genotypes existing in the focal population, in other populations, or even in closely related species. The second approach (called de novo adaptation approach) aims to generate new pre-adapted genotypes from the diversity present in the species through artificial selection. For each approach, we present a stage-by-stage procedure, with some techniques that can be used for its implementation. The associated risks and difficulties of each approach are also discussed.
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Affiliation(s)
- Elena Torres
- Departamento de Biotecnología-Biología Vegetal, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Alfredo García-Fernández
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Diana Iñigo
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Carlos Lara-Romero
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Javier Morente-López
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Grupo de Investigación de Ecología y Evolución en Islas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38206 Tenerife, Spain
| | - Samuel Prieto-Benítez
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Ecotoxicology of Air Pollution, Environmental Department, CIEMAT, 28040 Madrid, Spain
| | - María Luisa Rubio Teso
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - José M. Iriondo
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
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Contrasting patterns of population structure of Bulwer's petrel (Bulweria bulwerii) between oceans revealed by statistical phylogeography. Sci Rep 2023; 13:1939. [PMID: 36732530 PMCID: PMC9895040 DOI: 10.1038/s41598-023-28452-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/18/2023] [Indexed: 02/04/2023] Open
Abstract
The patterns of population divergence of mid-latitude marine birds are impacted by only a few biogeographic barriers to dispersal and the effect of intrinsic factors, such as fidelity to natal colonies or wintering grounds, may become more conspicuous. Here we describe, for the first time, the phylogeographic patterns and historical demography of Bulwer's petrel Bulweria bulwerii and provide new insights regarding the drivers of species diversification in the marine environment. We sampled Bulwer's petrels from the main breeding colonies and used a statistical phylogeography approach based on surveying nuclear and mitochondrial loci (~ 9100 bp) to study its mechanisms of global diversification. We uncovered three highly differentiated groups including the Western Pacific, the Central Pacific and the Atlantic. The older divergence occurred within the Pacific Ocean, ca. 850,000 ya, and since then the W Pacific group has been evolving in isolation. Conversely, divergence between the Central Pacific and Atlantic populations occurred within the last 200,000 years. While the Isthmus of Panama is important in restricting gene flow between oceans in Bulwer's petrels, the deepest phylogeographic break is within the Pacific Ocean, where oceanographic barriers are key in driving and maintaining the remarkable structure found in this highly mobile seabird. This is in contrast with the Atlantic, where no structure was detected. Further data will provide insights regarding the extent of lineage divergence of Bulwer's petrels in the Western Pacific.
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Varaldo L, Guerrina M, Dagnino D, Minuto L, Casazza G. Dealing with disjunct populations of vascular plants: implications for assessing the effect of climate change. Oecologia 2023; 201:421-434. [PMID: 36738314 PMCID: PMC9945546 DOI: 10.1007/s00442-023-05323-y] [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: 11/30/2021] [Accepted: 01/15/2023] [Indexed: 02/05/2023]
Abstract
Species distribution models are the most widely used tool to predict species distributions for species conservation and assessment of climate change impact. However, they usually do not consider intraspecific ecological variation exhibited by many species. Overlooking the potential differentiation among groups of populations may lead to misplacing any conservation actions. This issue may be particularly relevant in species in which few populations with potential local adaptation occur, as in species with disjunct populations. Here, we used ecological niche modeling to analyze how the projections of current and future climatically suitable areas of 12 plant species can be affected using the whole taxa occurrences compared to occurrences from geographically disjunct populations. Niche analyses suggest that usually the disjunct group of populations selects the climatic conditions as similar as possible to the other according to climate availability. Integrating intraspecific variability only slightly increases models' ability to predict species occurrences. However, it results in different predictions of the magnitude of range change. In some species, integrating or not integrating intraspecific variability may lead to opposite trend in projected range change. Our results suggest that integrating intraspecific variability does not strongly improve overall models' accuracy, but it can result in considerably different conclusions about future range change. Consequently, accounting for intraspecific differentiation may enable the detection of potential local adaptations to new climate and so to design targeted conservation strategies.
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Affiliation(s)
- Lucia Varaldo
- Università di Genova, Dipartimento di Scienze della terra, Ambiente e Vita, Corso Europa 26, I-16132, Genoa, Italy
| | - Maria Guerrina
- Università di Genova, Dipartimento di Scienze della terra, Ambiente e Vita, Corso Europa 26, I-16132, Genoa, Italy
| | - Davide Dagnino
- Università di Genova, Dipartimento di Scienze della terra, Ambiente e Vita, Corso Europa 26, I-16132, Genoa, Italy
| | - Luigi Minuto
- Università di Genova, Dipartimento di Scienze della terra, Ambiente e Vita, Corso Europa 26, I-16132, Genoa, Italy.
| | - Gabriele Casazza
- Università di Genova, Dipartimento di Scienze della terra, Ambiente e Vita, Corso Europa 26, I-16132, Genoa, Italy
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Khasanova A, Edwards J, Bonnette J, Singer E, Haque T, Juenger TE. Quantitative genetic-by-soil microbiome interactions in a perennial grass affect functional traits. Proc Biol Sci 2023; 290:20221350. [PMID: 36651054 PMCID: PMC9845970 DOI: 10.1098/rspb.2022.1350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Plants interact with diverse microbiomes that can impact plant growth and performance. Recent studies highlight the potential beneficial aspects of plant microbiomes, including the possibility that microbes facilitate the process of local adaptation in their host plants. Microbially mediated local adaptation in plants occurs when local host genotypes have higher fitness than foreign genotypes because of their affiliation with locally beneficial microbes. Here, plant adaptation results from genetic interactions of the host with locally beneficial microbes (e.g. host genotype-by-microbiome interactions). We used a recombinant inbred line (RIL) mapping population derived from upland and lowland ecotypes of the diploid C4 perennial bunch grass Panicum hallii to explore quantitative genetic responses to soil microbiomes focusing on functional root and shoot traits involved in ecotypic divergence. We show that the growth and development of ecotypes and their trait divergence depends on soil microbiomes. Moreover, we find that the genetic architecture is modified by soil microbiomes, revealing important plant genotype-by-microbiome interactions for quantitative traits. We detected a number of quantitative trait loci (QTL) that interact with the soil microbiome. Our results highlight the importance of microbial interactions in ecotypic divergence and trait genetic architecture in C4 perennial grasses.
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Affiliation(s)
- Albina Khasanova
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78712, USA,Lawrence Berkeley National Laboratory, 717 Potter Street, Berkeley, CA 94710, USA
| | - Joseph Edwards
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78712, USA
| | - Jason Bonnette
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78712, USA
| | - Esther Singer
- Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA,Lawrence Berkeley National Laboratory, 717 Potter Street, Berkeley, CA 94710, USA
| | - Taslima Haque
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78712, USA
| | - Thomas E. Juenger
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78712, USA
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Gallegos C, Hodgins KA, Monro K. Climate adaptation and vulnerability of foundation species in a global change hotspot. Mol Ecol 2023; 32:1990-2004. [PMID: 36645732 DOI: 10.1111/mec.16848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023]
Abstract
Climate change is altering species ranges, and relative abundances within ranges, as populations become differentially adapted and vulnerable to the climates they face. Understanding present species ranges, whether species harbour and exchange adaptive variants, and how variants are distributed across landscapes undergoing rapid change, is therefore crucial to predicting responses to future climates and informing conservation strategies. Such insights are nonetheless lacking for most species of conservation concern. We assess genomic patterns of neutral variation, climate adaptation and climate vulnerability (offsets in predicted distributions of putatively adaptive variants across present and future landscapes) for sister foundation species, the marine tubeworms Galeolaria caespitosa and Galeolaria gemineoa, in a sentinel region for climate change impacts. We find that species are genetically isolated despite uncovering sympatry in their ranges, show parallel and nonparallel signals of thermal adaptation on spatial scales smaller than gene flow across their ranges, and are predicted to face different risks of maladaptation under future temperatures across their ranges. Our findings have implications for understanding local adaptation in the face of gene flow, and generate spatially explicit predictions for climatic disruption of adaptation and species distributions in coastal ecosystems that could guide experimental validation and conservation planning.
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Affiliation(s)
- Cristóbal Gallegos
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Keyne Monro
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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38
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Davis CL, Muñoz DJ, Amburgey SM, Dinsmore CR, Teitsworth EW, Miller DAW. Multistate model to estimate sex‐specific dispersal rates and distances for a wetland‐breeding amphibian population. Ecosphere 2023. [DOI: 10.1002/ecs2.4345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Courtney L. Davis
- Department of Ecosystem Science and Management Pennsylvania State University University Park Pennsylvania USA
- Intercollege Graduate Ecology Program, Pennsylvania State University University Park Pennsylvania USA
- Cornell Lab of Ornithology Cornell University Ithaca New York USA
| | - David J. Muñoz
- Department of Ecosystem Science and Management Pennsylvania State University University Park Pennsylvania USA
- Intercollege Graduate Ecology Program, Pennsylvania State University University Park Pennsylvania USA
| | - Staci M. Amburgey
- Washington Cooperative Fish and Wildlife Research Unit, School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
- Washington Department of Fish and Wildlife Olympia Washington USA
| | - Carli R. Dinsmore
- Department of Ecosystem Science and Management Pennsylvania State University University Park Pennsylvania USA
| | - Eric W. Teitsworth
- Department of Fisheries, Wildlife, and Conservation Biology North Carolina State University Raleigh North Carolina USA
| | - David A. W. Miller
- Department of Ecosystem Science and Management Pennsylvania State University University Park Pennsylvania USA
- Intercollege Graduate Ecology Program, Pennsylvania State University University Park Pennsylvania USA
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Snead AA, Clark RD. The Biological Hierarchy, Time, and Temporal 'Omics in Evolutionary Biology: A Perspective. Integr Comp Biol 2022; 62:1872-1886. [PMID: 36057775 DOI: 10.1093/icb/icac138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 01/05/2023] Open
Abstract
Sequencing data-genomics, transcriptomics, epigenomics, proteomics, and metabolomics-have revolutionized biological research, enabling a more detailed study of processes, ranging from subcellular to evolutionary, that drive biological organization. These processes, collectively, are responsible for generating patterns of phenotypic variation and can operate over dramatically different timescales (milliseconds to billions of years). While researchers often study phenotypic variation at specific levels of biological organization to isolate processes operating at that particular scale, the varying types of sequence data, or 'omics, can also provide complementary inferences to link molecular and phenotypic variation to produce an integrated view of evolutionary biology, ranging from molecular pathways to speciation. We briefly describe how 'omics has been used across biological levels and then demonstrate the utility of integrating different types of sequencing data across multiple biological levels within the same study to better understand biological phenomena. However, single-time-point studies cannot evaluate the temporal dynamics of these biological processes. Therefore, we put forward temporal 'omics as a framework that can better enable researchers to study the temporal dynamics of target processes. Temporal 'omics is not infallible, as the temporal sampling regime directly impacts inferential ability. Thus, we also discuss the role the temporal sampling regime plays in deriving inferences about the environmental conditions driving biological processes and provide examples that demonstrate the impact of the sampling regime on biological inference. Finally, we forecast the future of temporal 'omics by highlighting current methodological advancements that will enable temporal 'omics to be extended across species and timescales. We extend this discussion to using temporal multi-omics to integrate across the biological hierarchy to evaluate and link the temporal dynamics of processes that generate phenotypic variation.
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Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - René D Clark
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
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Shuyskaya E, Toderich K, Kolesnikov A, Prokofieva M, Lebedeva M. Effects of Vertically Heterogeneous Soil Salinity on Genetic Polymorphism and Productivity of the Widespread Halophyte Bassia prostrata. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010056. [PMID: 36676005 PMCID: PMC9866743 DOI: 10.3390/life13010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
Salinity is one of the environmental factors that affects both productivity and genetic diversity in plant species. Within the soil profile, salinity is a dynamic indicator and significantly changes with depth. The present study examined the effects of the vertical heterogeneity of soil salinity chemistry on the plant height, fresh and dry biomass accumulation, water content, level of genetic polymorphism, and observed and expected heterozygosity in seven populations of halophyte Bassia prostrata in natural habitats. Soil salinity ranged from slight (Ssalts = 0.11-0.25%) to extreme (Ssalts = 1.35-2.57%). The main contributors to salinity were Na+, Ca2+, and Mg2+. Multivariate analysis revealed that biomass accumulation is positively affected by moderate/high salinity in 20-60 cm soil layers, which may be associated with the salt required for the optimal growth of the halophyte B. prostrata. The formation of seed genetic diversity is negatively affected by slight/moderate salinity in the 0-40 cm layers. An increase in divalent ion content can reduce genetic diversity and increase the local adaptation of B. prostrata to magnesium-calcium sulfate salinity. The effect of the in-depth distribution of soil salinity on productivity and genetic diversity may be related to seasonal variables during biomass accumulation (summer) and seed formation (autumn).
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Affiliation(s)
- Elena Shuyskaya
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., 127276 Moscow, Russia
- Correspondence:
| | - Kristina Toderich
- International Platform for Dryland Research and Education, Tottori University, Tottori 680-0001, Japan
| | - Alexander Kolesnikov
- Institute of Forest Science, Russian Academy of Sciences, 143030 Uspenskoe, Russia
| | - Maria Prokofieva
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., 127276 Moscow, Russia
| | - Marina Lebedeva
- V.V. Dokuchaev Soil Science Institute, 7/2 Pyzhevsky per., 119017 Moscow, Russia
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Tigano A, Russello MA. The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid. Mol Ecol 2022; 31:6588-6604. [PMID: 36208020 DOI: 10.1111/mec.16724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 01/13/2023]
Abstract
Recent ecotypic differentiation provides unique opportunities to investigate the genomic basis and architecture of local adaptation, while offering insights into how species form and persist. Sockeye salmon (Oncorhynchus nerka) exhibit migratory and resident ("kokanee") ecotypes, which are further distinguished into shore-spawning and stream-spawning reproductive ecotypes. Here, we analysed 36 sockeye (stream-spawning) and kokanee (stream- and shore-spawning) genomes from a system where they co-occur and have recent common ancestry (Okanagan Lake/River in British Columbia, Canada) to investigate the genomic basis of reproductive and migratory behaviour. Examination of the genomic landscape of differentiation, differences in allele frequencies and genotype-phenotype associations revealed three main blocks of sequence differentiation on chromosomes 7, 12 and 20, associated with migratory behaviour, spawning location and spawning timing. Structural variants identified in these same areas suggest they could contribute to ecotypic differentiation directly as causal variants or via maintenance of their genomic architecture through recombination suppression mechanisms. Genes in these regions were related to spatial memory and swimming endurance (SYNGAP, TPM3), as well as eye and brain development (including SIX6), potentially associated with differences in migratory behaviour and visual habitats across spawning locations, respectively. Additional genes (GREB1L, ROCK1) identified here have been associated with timing of migration in other salmonids and could explain variation in timing of O. nerka spawning. Together, these results based on the joint analysis of sequence and structural variation represent a significant advance in our understanding of the genomic landscape of ecotypic differentiation at different stages in the speciation continuum.
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Affiliation(s)
- Anna Tigano
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Michael A Russello
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
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Weist P, Jentoft S, Tørresen OK, Schade FM, Pampoulie C, Krumme U, Hanel R. The role of genomic signatures of directional selection and demographic history in the population structure of a marine teleost with high gene flow. Ecol Evol 2022; 12:e9602. [PMID: 36514551 PMCID: PMC9731920 DOI: 10.1002/ece3.9602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 11/14/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Recent studies have uncovered patterns of genomic divergence in marine teleosts where panmixia due to high gene flow has been the general paradigm. These signatures of divergent selection are often impacted by structural variants, acting as "supergenes" facilitating local adaptation. The highly dispersing European plaice (Pleuronectes platessa)-in which putative structural variants (i.e., inversions) have been identified-has successfully colonized the brackish water ecosystem of the Baltic Sea. Thus, the species represents an ideal opportunity to investigate how the interplay of gene flow, structural variants, natural selection, past demographic history, and gene flow impacts on population (sub)structuring in marine systems. Here, we report on the generation of an annotated draft plaice genome assembly in combination with population sequencing data-following the salinity gradient from the Baltic Sea into the North Sea together with samples from Icelandic waters-to illuminate genome-wide patterns of divergence. Neutral markers pointed at large-scale panmixia across the European continental shelf associated with high gene flow and a common postglacial colonization history of shelf populations. However, based on genome-wide outlier loci, we uncovered signatures of population substructuring among the European continental shelf populations, i.e., suggesting signs of ongoing selection. Genome-wide selection analyses (xp-EHH) and the identification of genes within genomic regions of recent selective sweeps-overlapping with the outlier loci-suggest that these represent the signs of divergent selection. Our findings provide support for genomic divergence driven by local adaptation in the face of high gene flow and elucidate the relative importance of demographic history versus adaptive divergence in shaping the contemporary population genetic structure of a marine teleost. The role of the putative inversion(s) in the substructuring-and potentially ongoing adaptation-was seemingly not substantial.
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Affiliation(s)
- Peggy Weist
- Thünen Institute of Fisheries EcologyBremerhavenGermany
| | - Sissel Jentoft
- Department of Biosciences, Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | - Ole K. Tørresen
- Department of Biosciences, Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | | | | | - Uwe Krumme
- Thünen Institute of Baltic Sea FisheriesRostockGermany
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Mijangos JL, Bino G, Hawke T, Kolomyjec SH, Kingsford RT, Sidhu H, Grant T, Day J, Dias KN, Gongora J, Sherwin WB. Fragmentation by major dams and implications for the future viability of platypus populations. Commun Biol 2022; 5:1127. [PMID: 36329312 PMCID: PMC9633709 DOI: 10.1038/s42003-022-04038-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
The evolutionarily unique platypus (Ornithorhynchus anatinus) has experienced major declines and extinctions from a range of historical and recent interacting human-mediated threats. Although spending most of their time in the water, platypuses can move over land. Nevertheless, uncertainties remain whether dams are barriers to movement, thus limiting gene flow and dispersal, essential to evolution and ecology. Here we examined disruption of gene flow between platypus groups below and above five major dams, matched to four adjacent rivers without major dams. Genetic differentiation (FST) across dams was 4- to 20-fold higher than along similar stretches of adjacent undammed rivers; FST across dams was similar to differentiation between adjacent river systems. This indicates that major dams represent major barriers for platypus movements. Furthermore, FST between groups was correlated with the year in which the dam was built, increasing by 0.011 every generation, reflecting the effects of these barriers on platypus genetics. This study provides evidence of gene flow restriction, which jeopardises the long-term viability of platypus populations when groups are fragmented by major dams. Mitigation strategies, such as building of by-pass structures and translocation between upstream and downstream of the dam, should be considered in conservation and management planning.
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Affiliation(s)
- Jose L. Mijangos
- grid.1005.40000 0004 4902 0432School of Science, UNSW, Canberra, Australia ,grid.1039.b0000 0004 0385 7472Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Gilad Bino
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Tahneal Hawke
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Stephen H. Kolomyjec
- grid.258898.60000 0004 0462 9201College of Science and the Environment, Lake Superior State University, Sault Sainte Marie, USA
| | - Richard T. Kingsford
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Harvinder Sidhu
- grid.1005.40000 0004 4902 0432School of Science, UNSW, Canberra, Australia
| | - Tom Grant
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Jenna Day
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - Kimberly N. Dias
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - Jaime Gongora
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - William B. Sherwin
- grid.1005.40000 0004 4902 0432Evolution & Ecology Research Centre, UNSW, Sydney, Australia
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44
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Dimitrova A, Csilléry K, Klisz M, Lévesque M, Heinrichs S, Cailleret M, Andivia E, Madsen P, Böhenius H, Cvjetkovic B, De Cuyper B, de Dato G, Ferus P, Heinze B, Ivetić V, Köbölkuti Z, Lazarević J, Lazdina D, Maaten T, Makovskis K, Milovanović J, Monteiro AT, Nonić M, Place S, Puchalka R, Montagnoli A. Risks, benefits, and knowledge gaps of non-native tree species in Europe. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.908464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Changing ecosystem conditions and diverse socio-economical events have contributed to an ingrained presence of non-native tree species (NNTs) in the natural and cultural European landscapes. Recent research endeavors have focused on different aspects of NNTs such as legislation, benefits, and risks for forestry, emphasizing that large knowledge gaps remain. As an attempt to fulfill part of these gaps, within the PEN-CAFoRR COST Action (CA19128) network, we established an open-access questionnaire that allows both academic experts and practitioners to provide information regarding NNTs from 20 European countries. Then, we integrated the data originating from the questionnaire, related to the country-based assessment of both peer-reviewed and grey literature, with information from available datasets (EUFORGEN and EU-Forest), which gave the main structure to the study and led to a mixed approach review. Finally, our study provided important insights into the current state of knowledge regarding NNTs. In particular, we highlighted NNTs that have shown to be less commonly addressed in research, raising caution about those characterized by an invasive behavior and used for specific purposes (e.g., wood production, soil recultivation, afforestation, and reforestation). NNTs were especially explored in the context of resilient and adaptive forest management. Moreover, we emphasized the assisted and natural northward migration of NNTs as another underscored pressing issue, which needs to be addressed by joint efforts, especially in the context of the hybridization potential. This study represents an additional effort toward the knowledge enhancement of the NNTs situation in Europe, aiming for a continuously active common source deriving from interprofessional collaboration.
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Common LK, Kleindorfer S, Colombelli-Négrel D, Dudaniec RY. Genetics reveals shifts in reproductive behaviour of the invasive bird parasite Philornis downsi collected from Darwin’s finch nests. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02935-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
AbstractDue to novel or dynamic fluctuations in environmental conditions and resources, host and parasite relationships can be subject to diverse selection pressures that may lead to significant changes during and after invasion of a parasite. Genomic analyses are useful for elucidating evolutionary processes in invasive parasites following their arrival to a new area and host. Philornis downsi (Diptera: Muscidae), the avian vampire fly, was introduced to the Galápagos Islands circa 1964 and has since spread across the archipelago, feeding on the blood of developing nestlings of endemic land birds. Since its discovery, there have been significant changes to the dynamics of P. downsi and its novel hosts, such as shifting mortality rates and changing oviposition behaviour, however no temporal genetic studies have been conducted. We collected P. downsi from nests and traps from a single island population over a 14-year period, and genotyped flies at 469 single nucleotide polymorphisms (SNPs) using restriction-site associated DNA sequencing (RADSeq). Despite significant genetic differentiation (FST) between years, there was no evidence for genetic clustering within or across four sampling years between 2006 and 2020, suggesting a lack of population isolation. Sibship reconstructions from P. downsi collected from 10 Darwin’s finch nests sampled in 2020 showed evidence for shifts in reproductive behaviour compared to a similar genetic analysis conducted in 2004–2006. Compared with this previous study, females mated with fewer males, individual females oviposited fewer offspring per nest, but more unique females oviposited per nest. These findings are important to consider within reproductive control techniques, and have fitness implications for both parasite evolution and host fitness.
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46
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Jiang N, Li Z, Dai Y, Liu Z, Han X, Li Y, Li Y, Xiong H, Xu J, Zhang G, Xiao S, Yuan X, Fu Y. Massive genome investigations reveal insights of prevalent introgression for environmental adaptation and triterpene biosynthesis in Ganoderma. Mol Ecol Resour 2022. [PMID: 36214617 DOI: 10.1111/1755-0998.13718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/26/2022] [Accepted: 10/06/2022] [Indexed: 11/29/2022]
Abstract
Genome introgression is one of the driving forces that can increase species and genetic diversity and facilitate the adaptive evolution of organisms and biodiversity conservation. However, the genomic introgression and its contribution to biodiversity of macrofungi are still unclear. The genus Ganoderma is a typical macrofungal group that plays crucial roles in forest ecosystem as saprophytic organisms and plant pathogens, and is also involved in human health as medicinal mushrooms. Most public Ganoderma genomes are fragmented, and reference genomes and whole-genome information of diverse germplasm resources for many Ganoderma species are lacking, thus hindering functional and evolutionary genomic investigations among Ganoderma species. In this study, we provide high-quality genomes of 10 Ganoderma species and whole-genome variants data of 224 individuals from various ecoregions, enabling us to infer the phylogeny of Ganoderma species and their historical population dynamics. Based on whole-genome variants, widespread and genome-wide introgression among Ganoderma species is revealed. Genes with significant introgression signals were related to stress response, digestive absorption, and secondary metabolite synthesis, factors that may contribute to environmental adaptation and important biocomponent metabolism. CYP512U6, an essential functional gene in the CYP450 family related to Ganoderma triterpene synthesis, was detected with significant introgression and selection signals combined with Ganoderma metabolomic analysis, indicating that both ancient gene exchange and recent domestication have contributed to the categories and content of secondary metabolites of Ganoderma. The reference genomes, whole-genome variants, and metabolite profiles could serve as abundant and valuable genetic resources for evolution, ecology, and conservation investigations of Ganoderma species and other macrofungi.
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Affiliation(s)
- Nan Jiang
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
- College of Plant Protection, Jilin Agricultural University, Jilin, Changchun, China
| | - Zhenhao Li
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Yueting Dai
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Zhenhua Liu
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Xuerong Han
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Yu Li
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Yong Li
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Hui Xiong
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Jing Xu
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Guoliang Zhang
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Shijun Xiao
- Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, Jiaxing, Zhejiang, China
| | - Xiaohui Yuan
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Yongping Fu
- College of Plant Protection, Jilin Agricultural University, Jilin, Changchun, China
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47
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Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. Evolution 2022; 76:2332-2346. [PMID: 35994296 PMCID: PMC9826283 DOI: 10.1111/evo.14602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/24/2022] [Accepted: 07/23/2022] [Indexed: 01/22/2023]
Abstract
Chromosomal inversions have been shown to play a major role in a local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.
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Affiliation(s)
- Eva L. Koch
- School of BiosciencesUniversity of SheffieldSheffieldUK,Department of ZoologyUniversity of CambridgeCambridgeUK
| | - Mark Ravinet
- School of Life SciencesUniversity of NottinghamNottinghamUK
| | - Anja M. Westram
- Institute of Science and Technology Austria (ISTA)KlosterneuburgAustria,Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Kerstin Johannesson
- Marine Science, Tjärnö Marine LaboratoryUniversity of GothenburgGothenburgSweden
| | - Roger K. Butlin
- School of BiosciencesUniversity of SheffieldSheffieldUK,Marine Science, Tjärnö Marine LaboratoryUniversity of GothenburgGothenburgSweden
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48
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Jackson N, Littleford-Colquhoun BL, Strickland K, Class B, Frere CH. Selection in the city: Rapid and fine-scale evolution of urban eastern water dragons. Evolution 2022; 76:2302-2314. [PMID: 35971751 DOI: 10.1111/evo.14596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/27/2022] [Accepted: 07/18/2022] [Indexed: 01/22/2023]
Abstract
Oceanic archipelagos have long been treated as a Petri dish for studies of evolutionary and ecological processes. Like archipelagos, cities exhibit similar patterns and processes, such as the rapid phenotypic divergence of a species between urban and nonurban environments. However, on a local scale, cities can be highly heterogenous, where geographically close populations can experience dramatically different environmental conditions. Nevertheless, we are yet to understand the evolutionary and ecological implications for populations spread across a heterogenous cityscape. To address this, we compared neutral genetic divergence to quantitative trait divergence within three native riparian and four city park populations of an iconic urban adapter, the eastern water dragon. We demonstrated that selection is likely acting to drive divergence of snout-vent length and jaw width across native riparian populations that are geographically isolated and across city park populations that are geographically close yet isolated by urbanization. City park populations as close as 0.9 km exhibited signs of selection-driven divergence to the same extent as native riparian populations isolated by up to 114.5 km. These findings suggest that local adaptation may be occurring over exceptionally small geographic and temporal scales within a single metropolis, demonstrating that city parks can act as archipelagos for the study of rapid evolution.
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Affiliation(s)
- Nicola Jackson
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Bethan L Littleford-Colquhoun
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island, 02912, US.,Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, 02912, US
| | - Kasha Strickland
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,Department of Aquaculture and Fish Biology, Hólar University, Sauðarkrókur, 550, Iceland
| | - Barbara Class
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Celine H Frere
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,School of Biological Sciences, University of Queensland, St. Lucia, QLD, 4072, Australia
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49
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Genomic basis of insularity and ecological divergence in barn owls (Tyto alba) of the Canary Islands. Heredity (Edinb) 2022; 129:281-294. [PMID: 36175501 PMCID: PMC9613907 DOI: 10.1038/s41437-022-00562-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 11/14/2022] Open
Abstract
Islands, and the particular organisms that populate them, have long fascinated biologists. Due to their isolation, islands offer unique opportunities to study the effect of neutral and adaptive mechanisms in determining genomic and phenotypical divergence. In the Canary Islands, an archipelago rich in endemics, the barn owl (Tyto alba), present in all the islands, is thought to have diverged into a subspecies (T. a. gracilirostris) on the eastern ones, Fuerteventura and Lanzarote. Taking advantage of 40 whole-genomes and modern population genomics tools, we provide the first look at the origin and genetic makeup of barn owls of this archipelago. We show that the Canaries hold diverse, long-standing and monophyletic populations with a neat distinction of gene pools from the different islands. Using a new method, less sensitive to structure than classical FST, to detect regions involved in local adaptation to insular environments, we identified a haplotype-like region likely under selection in all Canaries individuals and genes in this region suggest morphological adaptations to insularity. In the eastern islands, where the subspecies is present, genomic traces of selection pinpoint signs of adapted body proportions and blood pressure, consistent with the smaller size of this population living in a hot arid climate. In turn, genomic regions under selection in the western barn owls from Tenerife showed an enrichment in genes linked to hypoxia, a potential response to inhabiting a small island with a marked altitudinal gradient. Our results illustrate the interplay of neutral and adaptive forces in shaping divergence and early onset speciation.
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50
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Population Epigenetics: The Extent of DNA Methylation Variation in Wild Animal Populations. EPIGENOMES 2022; 6:epigenomes6040031. [PMID: 36278677 PMCID: PMC9589984 DOI: 10.3390/epigenomes6040031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Population epigenetics explores the extent of epigenetic variation and its dynamics in natural populations encountering changing environmental conditions. In contrast to population genetics, the basic concepts of this field are still in their early stages, especially in animal populations. Epigenetic variation may play a crucial role in phenotypic plasticity and local adaptation as it can be affected by the environment, it is likely to have higher spontaneous mutation rate than nucleotide sequences do, and it may be inherited via non-mendelian processes. In this review, we aim to bring together natural animal population epigenetic studies to generate new insights into ecological epigenetics and its evolutionary implications. We first provide an overview of the extent of DNA methylation variation and its autonomy from genetic variation in wild animal population. Second, we discuss DNA methylation dynamics which create observed epigenetic population structures by including basic population genetics processes. Then, we highlight the relevance of DNA methylation variation as an evolutionary mechanism in the extended evolutionary synthesis. Finally, we suggest new research directions by highlighting gaps in the knowledge of the population epigenetics field. As for our results, DNA methylation diversity was found to reveal parameters that can be used to characterize natural animal populations. Some concepts of population genetics dynamics can be applied to explain the observed epigenetic structure in natural animal populations. The set of recent advancements in ecological epigenetics, especially in transgenerational epigenetic inheritance in wild animal population, might reshape the way ecologists generate predictive models of the capacity of organisms to adapt to changing environments.
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