1
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Horníková M, Lanier HC, Marková S, Escalante MA, Searle JB, Kotlík P. Genetic admixture drives climate adaptation in the bank vole. Commun Biol 2024; 7:863. [PMID: 39009753 PMCID: PMC11251159 DOI: 10.1038/s42003-024-06549-z] [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: 07/20/2023] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
Genetic admixture introduces new variants at relatively high frequencies, potentially aiding rapid responses to environmental changes. Here, we evaluate its role in adaptive variation related to climatic conditions in bank voles (Clethrionomys glareolus) in Britain, using whole-genome data. Our results reveal loci showing excess ancestry from one of the two postglacial colonist populations inconsistent with overall admixture patterns. Notably, loci associated with climate adaptation exhibit disproportionate amounts of excess ancestry, highlighting the impact of admixture between colonist populations on local adaptation. The results suggest strong and localized selection on climate-adaptive loci, as indicated by steep clines and/or shifted cline centres, during population replacement. A subset, including a haemoglobin gene, is associated with oxidative stress responses, underscoring a role of oxidative stress in local adaptation. Our study highlights the important contribution of admixture during secondary contact between populations from distinct climatic refugia enriching adaptive diversity. Understanding these dynamics is crucial for predicting future adaptive capacity to anthropogenic climate change.
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Affiliation(s)
- Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Hayley C Lanier
- Department of Biology, Program in Ecology & Evolutionary Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Museum, University of Oklahoma, Norman, OK, USA
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.
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2
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Bell KL, Noreuil A, Molloy EK, Fritz ML. Genetic and behavioral differences between above and below ground Culex pipiens bioforms. Heredity (Edinb) 2024; 132:221-231. [PMID: 38424351 PMCID: PMC11074123 DOI: 10.1038/s41437-024-00675-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/26/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Efficiency of mosquito-borne disease transmission is dependent upon both the preference and fidelity of mosquitoes as they seek the blood of vertebrate hosts. While mosquitoes select their blood hosts through multi-modal integration of sensory cues, host-seeking is primarily an odor-guided behavior. Differences in mosquito responses to hosts and their odors have been demonstrated to have a genetic component, but the underlying genomic architecture of these responses has yet to be fully resolved. Here, we provide the first characterization of the genomic architecture of host preference in the polymorphic mosquito species, Culex pipiens. The species exists as two morphologically identical bioforms, each with distinct avian and mammalian host preferences. Cx. pipiens females with empirically measured host responses were prepared into reduced representation DNA libraries and sequenced to identify genomic regions associated with host preference. Multiple genomic regions associated with host preference were identified on all 3 Culex chromosomes, and these genomic regions contained clusters of chemosensory genes, as expected based on work in Anopheles gambiae complex mosquitoes and in Aedes aegypti. One odorant receptor and one odorant binding protein gene showed one-to-one orthologous relationships to differentially expressed genes in A. gambiae complex members with divergent host preferences. Overall, our work identifies a distinct set of odorant receptors and odorant binding proteins that may enable Cx. pipiens females to distinguish between their vertebrate blood host species, and opens avenues for future functional studies that could measure the unique contributions of each gene to host preference phenotypes.
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Affiliation(s)
- Katherine L Bell
- Department of Biology, University of Nevada, Reno, NV, 89557, USA.
| | - Anna Noreuil
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA
| | - Erin K Molloy
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Megan L Fritz
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA.
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3
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Wessinger CA. How the switch to hummingbird pollination has greatly contributed to our understanding of evolutionary processes. THE NEW PHYTOLOGIST 2024; 241:59-64. [PMID: 37853523 PMCID: PMC10843001 DOI: 10.1111/nph.19335] [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: 08/04/2023] [Accepted: 09/30/2023] [Indexed: 10/20/2023]
Abstract
The evolutionary switch to hummingbird pollination exemplifies complex adaptation, requiring evolutionary change in multiple component traits. Despite this complexity, diverse lineages have converged on hummingbird-adapted flowers on a relatively short evolutionary timescale. Here, I review how features of the genetic basis of adaptation contribute to this remarkable evolutionary lability. Large-effect substitutions, large mutational targets for adaptation, adaptive introgression, and concentrated architecture all contribute to the origin and maintenance of hummingbird-adapted flowers. The genetic features of adaptation are likely shaped by the ecological and geographic context of the switch to hummingbird pollination, with implications for future evolutionary trajectories.
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Affiliation(s)
- Carolyn A Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
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4
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Firneno TJ, Semenov G, Dopman EB, Taylor SA, Larson EL, Gompert Z. Quantitative Analyses of Coupling in Hybrid Zones. Cold Spring Harb Perspect Biol 2023; 15:a041434. [PMID: 37739809 PMCID: PMC10691479 DOI: 10.1101/cshperspect.a041434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
In hybrid zones, whether barrier loci experience selection mostly independently or as a unit depends on the ratio of selection to recombination as captured by the coupling coefficient. Theory predicts a sharper transition between an uncoupled and coupled system when more loci affect hybrid fitness. However, the extent of coupling in hybrid zones has rarely been quantified. Here, we use simulations to characterize the relationship between the coupling coefficient and variance in clines across genetic loci. We then reanalyze 25 hybrid zone data sets and find that cline variances and estimated coupling coefficients form a smooth continuum from high variance and weak coupling to low variance and strong coupling. Our results are consistent with low rates of hybridization and a strong genome-wide barrier to gene flow when the coupling coefficient is much greater than 1, but also suggest that this boundary might be approached gradually and at a near constant rate over time.
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Affiliation(s)
- Thomas J Firneno
- Department of Biology, University of Denver, Denver, Colorado 80208, USA
| | - Georgy Semenov
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80211, USA
| | - Erik B Dopman
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80211, USA
| | - Erica L Larson
- Department of Biology, University of Denver, Denver, Colorado 80208, USA
| | - Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah 84321, USA
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5
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Harrison M, Sotola VA, Zalmat A, Sullivan KT, Littrell BM, Bonner TH, Martin NH. A Comparison of Non-Destructive Visceral Swab and Tissue Biopsy Sampling Methods for Genotyping-by-Sequencing in the Freshwater Mussel Fusconaia askewi. Genes (Basel) 2023; 14:1197. [PMID: 37372377 DOI: 10.3390/genes14061197] [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: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Limiting harm to organisms caused by genetic sampling is an important consideration for rare species, and a number of non-destructive sampling techniques have been developed to address this issue in freshwater mussels. Two methods, visceral swabbing and tissue biopsies, have proven to be effective for DNA sampling, though it is unclear as to which method is preferable for genotyping-by-sequencing (GBS). Tissue biopsies may cause undue stress and damage to organisms, while visceral swabbing potentially reduces the chance of such harm. Our study compared the efficacy of these two DNA sampling methods for generating GBS data for the unionid freshwater mussel, the Texas pigtoe (Fusconaia askewi). Our results find both methods generate quality sequence data, though some considerations are in order. Tissue biopsies produced significantly higher DNA concentrations and larger numbers of reads when compared with swabs, though there was no significant association between starting DNA concentration and number of reads generated. Swabbing produced greater sequence depth (more reads per sequence), while tissue biopsies revealed greater coverage across the genome (at lower sequence depth). Patterns of genomic variation as characterized in principal component analyses were similar regardless of the sampling method, suggesting that the less invasive swabbing is a viable option for producing quality GBS data in these organisms.
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Affiliation(s)
- Matthew Harrison
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - V Alex Sotola
- Biology Department, State University of New York at Oneonta, 108 Ravine Parkway, Oneonta, NY 13820, USA
| | - Alexander Zalmat
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Kyle T Sullivan
- BIO-WEST, Inc., 1405 United Drive, Suite 111, San Marcos, TX 78666, USA
| | | | - Timothy H Bonner
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Noland H Martin
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
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6
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DeVos TB, Bock DG, Kolbe JJ. Rapid introgression of non-native alleles following hybridization between a native Anolis lizard species and a cryptic invader across an urban landscape. Mol Ecol 2023; 32:2930-2944. [PMID: 36811388 DOI: 10.1111/mec.16897] [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: 03/08/2022] [Revised: 02/14/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
Invasive species can impact native populations through competition, predation, habitat alteration, and disease transmission, but also genetically through hybridization. Potential outcomes of hybridization span the continuum from extinction to hybrid speciation and can be further complicated by anthropogenic habitat disturbance. Hybridization between the native green anole lizard (Anolis carolinensis) and a morphologically similar invader (A. porcatus) in south Florida provides an ideal opportunity to study interspecific admixture across a heterogeneous landscape. We used reduced-representation sequencing to describe introgression in this hybrid system and to test for a relationship between urbanization and non-native ancestry. Our findings indicate that hybridization between green anole lineages was probably a limited, historic event, producing a hybrid population characterized by a diverse continuum of ancestry proportions. Genomic cline analyses revealed rapid introgression and disproportionate representation of non-native alleles at many loci and no evidence for reproductive isolation between parental species. Three loci were associated with urban habitat characteristics; urbanization and non-native ancestry were positively correlated, although this relationship did not remain significant when accounting for spatial nonindependence. Ultimately, our study demonstrates the persistence of non-native genetic material even in the absence of ongoing immigration, indicating that selection favouring non-native alleles can override the demographic limitation of low propagule pressure. We also note that not all outcomes of admixture between native and non-native species should be considered intrinsically negative. Hybridization with ecologically robust invaders can lead to adaptive introgression, which may facilitate the long-term survival of native populations otherwise unable to adapt to anthropogenically mediated global change.
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Affiliation(s)
- Tyler B DeVos
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Dan G Bock
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Jason J Kolbe
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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7
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Bruno Agudo A, Xavier Picó F, Mateo RG, Marcer A, Torices R, Álvarez I. Unravelling plant diversification: Intraspecific genetic differentiation in hybridizing Anacyclus species in the western Mediterranean Basin. AMERICAN JOURNAL OF BOTANY 2023; 110:e16121. [PMID: 36541247 DOI: 10.1002/ajb2.16121] [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: 03/04/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
PREMISE The interfertile species Anacyclus clavatus, A. homogamos, and A. valentinus represent a plant complex coexisting in large anthropic areas of the western Mediterranean Basin with phenotypically mixed populations exhibiting a great floral variation. The goal of this study was to estimate the genetic identity of each species, to infer the role of hybridization in the observed phenotypic diversity, and to explore the effect of climate on the geographic distribution of species and genetic clusters. METHODS We used eight nuclear microsatellites to genotype 585 individuals from 31 populations of three Anacyclus species for population genetic analyses by using clustering algorithms based on Bayesian models and ordination methods. In addition, we used ecological niche models and niche overlap analyses for both the species and genetic clusters. We used an expanded data set, including 721 individuals from 129 populations for ecological niche models of the genetic clusters. RESULTS We found a clear correspondence between species and genetic clusters, except for A. clavatus that included up to three genetic clusters. We detected individuals with admixed genetic ancestry in A. clavatus and in mixed populations. Ecological niche models predicted similar distributions for species and genetic clusters. For the two specific genetic clusters of A. clavatus, ecological niche models predicted remarkably different areas. CONCLUSIONS Gene flow between Anacyclus species likely explains phenotypic diversity in contact areas. In addition, we suggest that introgression could be involved in the origin of one of the two A. clavatus genetic clusters, which also showed ecological differentiation.
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Affiliation(s)
- A Bruno Agudo
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - F Xavier Picó
- Departamento de Ecología y Evolución, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Rubén G Mateo
- Departamento de Biología (Botánica), Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Arnald Marcer
- CREAF, E 08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
- Universitat Autònoma de Barcelona, E 08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
| | - Rubén Torices
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - Inés Álvarez
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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8
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Zalmat AS, Sotola VA, Nice CC, Martin NH. Genetic structure in Louisiana Iris species reveals patterns of recent and historical admixture. AMERICAN JOURNAL OF BOTANY 2021; 108:2257-2268. [PMID: 34618352 DOI: 10.1002/ajb2.1758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
PREMISE When divergent lineages come into secondary contact, reproductive isolation may be incomplete, thus providing an opportunity to investigate how speciation is manifested in the genome. The Louisiana Irises (Iris, series Hexagonae) comprise a group of three or more ecologically and reproductively divergent lineages that can produce hybrids where they come into contact. We estimated standing genetic variation to understand the current distribution of population structure in the Louisiana Irises. METHODS We used genotyping-by-sequencing techniques to sample the genomes of Louisiana Iris species across their ranges. We sampled 20 populations (n = 632 individuals) across 11,249 loci and used Entropy and PCA models to assess population genetic data. RESULTS We discovered evidence for interspecific gene flow in parts of the range. Our analysis revealed patterns of population structure at odds with widely accepted nominal taxonomy. We discovered undescribed hybrid populations, designated as belonging to the I. brevicaulis lineage. Iris nelsonii shared significant ancestry with only one of the purported parent species, I. fulva, evidence inconsistent with a hybrid origin. CONCLUSIONS This study provides several key findings important to the investigation of standing genetic variation in the Louisiana Iris species complex. Compared to the other nominal species, I. brevicaulis contains a large amount of genetic diversity. In addition, we discovered a previously unknown hybrid zone between I. brevicaulis and I. hexagona along the Texas coast. Finally, our results do not support the long-standing hypothesis that I. nelsonii has mixed ancestry from three parental taxa.
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Affiliation(s)
- Alexander S Zalmat
- Department of Biology, Texas State University, San Marcos, Texas, 78666-0202, USA
| | - V Alex Sotola
- Department of Genetics, University of Georgia, Athens, Georgia, 30602-7223, USA
| | - Chris C Nice
- Department of Biology, Texas State University, San Marcos, Texas, 78666-0202, USA
| | - Noland H Martin
- Department of Biology, Texas State University, San Marcos, Texas, 78666-0202, USA
- Director of the Population and Conservation Biology Program, Department of Biology, Texas State University, San Marcos, Texas, 78666-0202, USA
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9
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Jahner JP, Parchman TL, Matocq MD. Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition. Mol Ecol 2021; 30:4245-4258. [PMID: 34219316 DOI: 10.1111/mec.16056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/28/2021] [Indexed: 12/27/2022]
Abstract
When organisms experience secondary contact after allopatric divergence, genomic regions can introgress differentially depending on their relationships with adaptation, reproductive isolation, recombination, and drift. Analyses of genome-wide patterns of divergence and introgression could provide insight into the outcomes of hybridization and the potential relationship between allopatric divergence and reproductive isolation. Here, we generate population genetic data (26,262 SNPs; 353 individuals) using a reduced-representation sequencing approach to quantify patterns of ancestry, differentiation, and introgression between a pair of ecologically distinct mammals-the desert woodrat (N. lepida) and Bryant's woodrat (N. bryanti)-that hybridize at a sharp ecotone in southern California. Individual ancestry estimates confirmed that hybrids were rare in this bimodal hybrid zone, and entirely consisted of a few F1 individuals and a broad range of multigenerational backcrosses. Genomic cline analyses indicated more than half of loci had elevated introgression from one genomic background into the other. However, introgression was not associated with relative or absolute measures of divergence, and loci with extreme values for both were not typically found near detoxification enzymes previously implicated in dietary specialization for woodrats. The decoupling of differentiation and introgression suggests that processes other than adaptation, such as drift, may underlie the extreme clines at this contact zone.
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Affiliation(s)
- Joshua P Jahner
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA
| | - Marjorie D Matocq
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA.,Department of Natural Resources and Environmental Science, University of Nevada, Reno, Nevada, USA
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10
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McFarlane SE, Senn HV, Smith SL, Pemberton JM. Locus-specific introgression in young hybrid swarms: Drift may dominate selection. Mol Ecol 2021; 30:2104-2115. [PMID: 33638185 DOI: 10.1111/mec.15862] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/01/2021] [Accepted: 02/17/2021] [Indexed: 12/17/2022]
Abstract
Closely related species that have previously inhabited geographically separated ranges are hybridizing at an increasing rate due to human disruptions. These human-mediated hybrid zones can be used to study reproductive isolation between species at secondary contact, including examining locus-specific rates of introgression. Introgression is expected to be heterogenous across the genome, reflecting variation in selection. Those loci that introgress especially slowly are good candidates for being involved in reproductive isolation, while those loci that introgress quickly may be involved in adaptive introgression. In the context of conservation, policy makers are especially concerned about introduced alleles moving quickly into the background of a native or endemic species, as these alleles could replace the native alleles in the population, leading to extinction via hybridization. We applied genomic cline analyses to 44,997 SNPs to identify loci introgressing more or less when compared to the genome wide expectation in a human-mediated hybridizing population of red deer and sika in Kintyre Scotland. We found 11.4% of SNPs had cline centres that were significantly different from the genome wide expectation, and 17.6% of all SNPs had excess rates of introgression. Based on simulations, we believe that many of these markers have diverged from the genome-wide average due to drift, rather than because of selection, and we suggest that these simulations can be useful as a null distribution for future studies of genomic clines. Future work on red deer and sika could determine the policy implications of allelic-replacement due to drift rather than selection, and could use replicate, geographically distinct hybrid zones to narrow down those loci that are responding to selection.
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Affiliation(s)
- S Eryn McFarlane
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,Department of Biology, Lund University, Lund, Sweden
| | - Helen V Senn
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,WildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Stephanie L Smith
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, UK
| | - Josephine M Pemberton
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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11
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Mavrodiev EV, Gómez JP, Mavrodiev NE, Melton AE, Martínez‐Azorín M, Crespo MB, Robinson SK, Steadman DW. On biodiversity and conservation of the
Iris hexagona
complex (
Phaeiris
, Iridaceae). Ecosphere 2021. [DOI: 10.1002/ecs2.3331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Evgeny V. Mavrodiev
- Florida Museum of Natural History University of Florida PO Box 117800 Gainesville Florida32611USA
| | - Juan P. Gómez
- Departamento de Química y Biología Universidad del Norte Km 5 Vía a Pto. Colombia Barranquilla Colombia
| | | | - Anthony E. Melton
- Florida Museum of Natural History University of Florida PO Box 117800 Gainesville Florida32611USA
| | - Mario Martínez‐Azorín
- Departamento de Ciencias Ambientales y Recursos Naturales (Botánica) Universidad de Alicante Apartado 99 AlicanteE‐03080Spain
| | - Manuel B. Crespo
- Departamento de Ciencias Ambientales y Recursos Naturales (Botánica) Universidad de Alicante Apartado 99 AlicanteE‐03080Spain
| | - Scott K. Robinson
- Florida Museum of Natural History University of Florida PO Box 117800 Gainesville Florida32611USA
| | - David W. Steadman
- Florida Museum of Natural History University of Florida PO Box 117800 Gainesville Florida32611USA
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12
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Samad NA, Hidalgo O, Saliba E, Siljak-Yakovlev S, Strange K, Leitch IJ, Dagher-Kharrat MB. Genome Size Evolution and Dynamics in Iris, with Special Focus on the Section Oncocyclus. PLANTS 2020; 9:plants9121687. [PMID: 33271865 PMCID: PMC7760388 DOI: 10.3390/plants9121687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/21/2020] [Accepted: 11/26/2020] [Indexed: 12/27/2022]
Abstract
Insights into genome size dynamics and its evolutionary impact remain limited by the lack of data for many plant groups. One of these is the genus Iris, of which only 53 out of c. 260 species have available genome sizes. In this study, we estimated the C-values for 41 species and subspecies of Iris mainly from the Eastern Mediterranean region. We constructed a phylogenetic framework to shed light on the distribution of genome sizes across subgenera and sections of Iris. Finally, we tested evolutionary models to explore the mode and tempo of genome size evolution during the radiation of section Oncocyclus. Iris as a whole displayed a great variety of C-values; however, they were unequally distributed across the subgenera and sections, suggesting that lineage-specific patterns of genome size diversification have taken place within the genus. The evolutionary model that best fitted our data was the speciational model, as changes in genome size appeared to be mainly associated with speciation events. These results suggest that genome size dynamics may have contributed to the radiation of Oncocyclus irises. In addition, our phylogenetic analysis provided evidence that supports the segregation of the Lebanese population currently attributed to Iris persica as a distinct species.
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Affiliation(s)
- Nour Abdel Samad
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Campus Sciences et Technologies, Université Saint-Joseph, Mar Roukos, Mkalles, BP: 1514 Riad el Solh, Beirut 1107 2050, Lebanon; (N.A.S.); (E.S.)
- Ecologie Systématique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France;
| | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK; (K.S.); (I.J.L.)
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Spain
- Correspondence: (O.H.); (M.B.D.-K.)
| | - Elie Saliba
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Campus Sciences et Technologies, Université Saint-Joseph, Mar Roukos, Mkalles, BP: 1514 Riad el Solh, Beirut 1107 2050, Lebanon; (N.A.S.); (E.S.)
| | - Sonja Siljak-Yakovlev
- Ecologie Systématique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France;
| | - Kit Strange
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK; (K.S.); (I.J.L.)
| | - Ilia J. Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK; (K.S.); (I.J.L.)
| | - Magda Bou Dagher-Kharrat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Campus Sciences et Technologies, Université Saint-Joseph, Mar Roukos, Mkalles, BP: 1514 Riad el Solh, Beirut 1107 2050, Lebanon; (N.A.S.); (E.S.)
- Correspondence: (O.H.); (M.B.D.-K.)
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13
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Berdan EL, Fuller RC, Kozak GM. Genomic landscape of reproductive isolation in Lucania killifish: The role of sex loci and salinity. J Evol Biol 2020; 34:157-174. [PMID: 33118222 PMCID: PMC7894299 DOI: 10.1111/jeb.13725] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 10/01/2020] [Accepted: 10/14/2020] [Indexed: 01/24/2023]
Abstract
Adaptation to different environments can directly and indirectly generate reproductive isolation between species. Bluefin killifish (Lucania goodei) and rainwater killifish (L. parva) are sister species that have diverged across a salinity gradient and are reproductively isolated by habitat, behavioural, extrinsic and intrinsic post-zygotic isolation. We asked if salinity adaptation contributes indirectly to other forms of reproductive isolation via linked selection and hypothesized that low recombination regions, such as sex chromosomes or chromosomal rearrangements, might facilitate this process. We conducted QTL mapping in backcrosses between L. parva and L. goodei to explore the genetic architecture of salinity tolerance, behavioural isolation and intrinsic isolation. We mapped traits relative to a chromosome that has undergone a centric fusion in L. parva (relative to L. goodei). We found that the sex locus appears to be male determining (XX-XY), was located on the fused chromosome and was implicated in intrinsic isolation. QTL associated with salinity tolerance were spread across the genome and did not overly co-localize with regions associated with behavioural or intrinsic isolation. This preliminary analysis of the genetic architecture of reproductive isolation between Lucania species does not support the hypothesis that divergent natural selection for salinity tolerance led to behavioural and intrinsic isolation as a by-product. Combined with previous studies in this system, our work suggests that adaptation as a function of salinity contributes to habitat isolation and that reinforcement may have contributed to the evolution of behavioural isolation instead, possibly facilitated by linkage between behavioural isolation and intrinsic isolation loci on the fused chromosome.
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Affiliation(s)
- Emma L Berdan
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Rebecca C Fuller
- Department of Animal Biology, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Genevieve M Kozak
- Department of Biology, University of Massachusetts-Dartmouth, Dartmouth, MA, USA
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14
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İpekdal K, Burban C, Sauné L, Battisti A, Kerdelhué C. From refugia to contact: Pine processionary moth hybrid zone in a complex biogeographic setting. Ecol Evol 2020; 10:1623-1638. [PMID: 32076539 PMCID: PMC7029074 DOI: 10.1002/ece3.6018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/15/2022] Open
Abstract
Contact zones occur at the crossroad between specific dispersal routes and are facilitated by biogeographic discontinuities. Here, we focused on two Lepidoptera sister species that come in contact near the Turkish Straits System (TSS). We aimed to infer their phylogeographic histories in the Eastern Mediterranean and finely analyze their co-occurrence and hybridization patterns in this biogeographic context. We used molecular mitochondrial and nuclear markers to study 224 individuals from 42 localities. We used discordances between markers and complementary assignment methods to identify and map hybrids and parental individuals. We confirmed the parapatric distribution of Thaumetopoea pityocampa (Lepidoptera: Notodontidae) in the west and Thaumetopoea wilkinsoni in the east and identified a narrow contact zone. We identified several glacial refugia of T. wilkinsoni in southern Turkey with a strong east-west differentiation in this species. Unexpectedly, T. pityocampa crossed the TSS and occur in northern Aegean Turkey and some eastern Greek islands. We found robust evidence of introgression between the two species in a restricted zone in northwestern Turkey, but we did not identify any F1 individuals. The identified hybrid zone was mostly bimodal. The distributions and genetic patterns of the studied species were strongly influenced both by the Quaternary climatic oscillations and the complex geological history of the Aegean region. T. pityocampa and T. wilkinsoni survived the last glacial maximum in disjoint refugia and met in western Turkey at the edge of the recolonization routes. Expanding population of T. wilkinsoni constrained T. pityocampa to the western Turkish shore. Additionally, we found evidence of recurrent introgression by T. wilkinsoni males in several T. pityocampa populations. Our results suggest that some prezygotic isolation mechanisms, such as differences in timing of the adult emergences, might be a driver of the isolation between the sister species.
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Affiliation(s)
| | | | - Laure Sauné
- INRAE, CBGP (INRAE, CIRAD, RD, Montpellier Supagro, Univ. Montpellier)MontpellierFrance
| | | | - Carole Kerdelhué
- INRAE, CBGP (INRAE, CIRAD, RD, Montpellier Supagro, Univ. Montpellier)MontpellierFrance
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15
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Knief U, Bossu CM, Saino N, Hansson B, Poelstra J, Vijay N, Weissensteiner M, Wolf JBW. Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone. Nat Ecol Evol 2019; 3:570-576. [PMID: 30911146 PMCID: PMC6445362 DOI: 10.1038/s41559-019-0847-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/18/2019] [Indexed: 12/22/2022]
Abstract
The evolution of genetic barriers opposing inter-specific gene flow is key to the origin of new species. Drawing from information of over 400 admixed genomes sourced from replicate transects across the European hybrid zone between all-black carrion crows and grey-coated hooded crows, we decipher the interplay between phenotypic divergence and selection at the molecular level. Over 68% of plumage variation was explained by epistasis between the gene NDP and a ~2.8 Mb region on chromosome 18 with suppressed recombination. Both pigmentation loci showed evidence for divergent selection resisting introgression. This study reveals how few, large-effect loci can govern prezygotic isolation and shield phenotypic divergence from gene flow.
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Affiliation(s)
- Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany
| | - Christen M Bossu
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden.,Institute of the Environment and Sustainability, Center for Tropical Research, University of California, Los Angeles, CA, USA
| | - Nicola Saino
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
| | - Jelmer Poelstra
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Biology Department, Duke University, Durham, NC, USA
| | - Nagarjun Vijay
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Matthias Weissensteiner
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany.,Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany. .,Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.
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16
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Alex Sotola V, Ruppel DS, Bonner TH, Nice CC, Martin NH. Asymmetric introgression between fishes in the Red River basin of Texas is associated with variation in water quality. Ecol Evol 2019; 9:2083-2095. [PMID: 30847094 PMCID: PMC6392354 DOI: 10.1002/ece3.4901] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 01/01/2023] Open
Abstract
When ecologically divergent taxa encounter one another, hybrid zones can form when reproductive isolation is incomplete. The location of such hybrid zones can be influenced by environmental variables, and an ecological context can provide unique insights into the mechanisms by which species diverge and are maintained. Two ecologically differentiated species of small benthic fishes, the endemic and imperiled prairie chub, Macrhybopsis australis, and the shoal chub, Macrhybopsis hyostoma, are locally sympatric within the upper Red River Basin of Texas. We integrated population genomic data and environmental data to investigate species divergence and the maintenance of species boundaries in these two species. We found evidence of advanced-generation asymmetric hybridization and introgression, with shoal chub alleles introgressing more frequently into prairie chubs than the reciprocal. Using a Bayesian Genomic Cline framework, patterns of genomic introgression were revealed to be quite heterogeneous, yet shoal chub alleles were found to have likely selectively introgressed across species boundaries significantly more often than prairie chub alleles, potentially explaining some of the observed asymmetry in hybridization. These patterns were remarkably consistent across two sampled geographic regions of hybridization. Several environmental variables were found to significantly predict individual admixture, suggesting ecological isolation might maintain species boundaries.
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Affiliation(s)
| | | | | | - Chris C. Nice
- Biology DepartmentTexas State UniversitySan MarcosTexas
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17
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Taylor SA, Larson EL. Insights from genomes into the evolutionary importance and prevalence of hybridization in nature. Nat Ecol Evol 2019; 3:170-177. [DOI: 10.1038/s41559-018-0777-y] [Citation(s) in RCA: 211] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/04/2018] [Indexed: 01/27/2023]
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