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Woronowicz KC, Esin EV, Markevich GN, Martinez CS, McMenamin SK, Daane JM, Harris MP, Shkil FN. Phylogenomic analysis of the Lake Kronotskoe species flock of Dolly Varden charr reveals genetic and developmental signatures of sympatric radiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.24.529919. [PMID: 38712299 PMCID: PMC11071292 DOI: 10.1101/2023.02.24.529919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Recent adaptive radiations provide evolutionary case studies, which provide the context to parse the relationship between genomic variation and the origins of distinct phenotypes. Sympatric radiations of the charr complex (genus Salvelinus) present a trove for phylogenetics as charrs have repeatedly diversified into multiple morphs with distinct feeding specializations. However, species flocks normally comprise only two to three lineages. Dolly Varden charr inhabiting Lake Kronotske represent the most extensive radiation described for the charr genus, containing at least seven lineages, each with defining morphological and ecological traits. Here, we perform the first genome-wide analysis of this species flock to parse the foundations of adaptive change. Our data support distinct, reproductively isolated lineages with little evidence of hybridization. We also find that specific selection on thyroid signaling and craniofacial genes forms a genomic basis for the radiation. Thyroid hormone is further implicated in subsequent lineage partitioning events. These results delineate a clear genetic basis for the diversification of specialized lineages, and highlight the role of developmental mechanisms in shaping the forms generated during adaptive radiation.
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Affiliation(s)
- Katherine C Woronowicz
- Department of Orthopaedics, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Evgeny V Esin
- AN Severtsov Institute of Ecology and Evolution, RAS; Leninskiy-33, 119071 Moscow, Russian Federation
| | - Grigorii N Markevich
- Kronotsky Nature Biosphere Reserve; Ryabikova-48, 68400 Yelizovo, Russian Federation
| | | | | | - Jacob M Daane
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204
| | - Matthew P Harris
- Department of Orthopaedics, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Fedor N Shkil
- AN Severtsov Institute of Ecology and Evolution, RAS; Leninskiy-33, 119071 Moscow, Russian Federation
- NK Koltzov Institute of Developmental Biology, RAS; Vavilova-26, 119334 Moscow, Russian Federation
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2
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Sinaga P, Klichowska E, Nowak A, Nobis M. Hybridization and introgression events in cooccurring populations of closely related grasses (Poaceae: Stipa) in high mountain steppes of Central Asia. PLoS One 2024; 19:e0298760. [PMID: 38412151 PMCID: PMC10898772 DOI: 10.1371/journal.pone.0298760] [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: 10/31/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024] Open
Abstract
Stipa is a genus comprising ca. 150 species found in warm temperate regions of the Old World and around 30% of its representatives are of hybrid origin. In this study, using integrative taxonomy approach, we tested the hypothesis that hybridization and introgression are the explanations of the morphological intermediacy in species belonging to Stipa sect. Smirnovia, one of the species-rich sections in the mountains of Central Asia. Two novel nothospecies, S. magnifica × S. caucasica subsp. nikolai and S. lingua × S. caucasica subsp. nikolai, were identified based on a combination of morphological characters and SNPs markers. SNPs marker revealed that all S. lingua × S. caucasica samples were F1 hybrids, whereas most of S. magnifica × S. caucasica samples were backcross hybrids. Furthermore, the above mentioned hybrids exhibit transgressive morphological characters to each of their parental species. These findings have implications for understanding the process of hybridization in the genus Stipa, particularly in the sect. Smirnovia. As a taxonomic conclusion, we describe the two new nothospecies S. × muksuensis (from Tajikistan) and S. × ochyrae (from Kyrgyzstan) and present an identification key to species morphologically similar to the taxa mentioned above.
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Affiliation(s)
- Patar Sinaga
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Arkadiusz Nowak
- Polish Academy of Sciences Botanical Garden – Center for Biological Diversity Conservation in Powsin, Warszawa, Poland
- Botanical Garden of the Wrocław University, Wrocław, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
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3
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Venney CJ, Mérot C, Normandeau E, Rougeux C, Laporte M, Bernatchez L. Epigenetic and Genetic Differentiation Between Coregonus Species Pairs. Genome Biol Evol 2024; 16:evae013. [PMID: 38271269 PMCID: PMC10849188 DOI: 10.1093/gbe/evae013] [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: 07/06/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Phenotypic diversification is classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that DNA methylation is involved in evolutionary processes due to its phenotypic and transcriptional effects. Methylation can increase mutagenesis and could lead to increased genetic divergence between populations experiencing different environmental conditions for many generations, though there has been minimal empirical research on epigenetically induced mutagenesis in diversification and speciation. Whitefish, freshwater members of the salmonid family, are excellent systems to study phenotypic diversification and speciation due to the repeated divergence of benthic-limnetic species pairs serving as natural replicates. Here we investigate whole genome genetic and epigenetic differentiation between sympatric benthic-limnetic species pairs in lake and European whitefish (Coregonus clupeaformis and Coregonus lavaretus) from four lakes (N = 64). We found considerable, albeit variable, genetic and epigenetic differences between species pairs. All SNP types were enriched at CpG sites supporting the mutagenic nature of DNA methylation, though C>T SNPs were most common. We also found an enrichment of overlaps between outlier SNPs with the 5% highest FST between species and differentially methylated loci. This could possibly represent differentially methylated sites that have caused divergent genetic mutations between species, or divergent selection leading to both genetic and epigenetic variation at these sites. Our results support the hypothesis that DNA methylation contributes to phenotypic divergence and mutagenesis during whitefish speciation.
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Affiliation(s)
- Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- UMR 6553 Ecobio, OSUR, CNRS, Université de Rennes, Rennes, France
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Clément Rougeux
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Ministère des Forêts, de la Faune et des Parcs (MFFP), Québec, Québec, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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4
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Stone BW, Wessinger CA. Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression. Mol Biol Evol 2024; 41:msae007. [PMID: 38232726 PMCID: PMC10826641 DOI: 10.1093/molbev/msae007] [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: 11/01/2023] [Revised: 01/01/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024] Open
Abstract
Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations versus preexisting variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns of phylogenetic discordance and introgression in Penstemon subgenus Dasanthera, a small and diverse adaptive radiation of plants. We found that magenta hummingbird-adapted flowers have apparently evolved twice from ancestral blue-violet bee-pollinated flowers within this radiation. These shifts in flower color are accompanied by a variety of inactivating mutations to a key anthocyanin pathway enzyme, suggesting that independent de novo loss-of-function mutations underlie the parallel evolution of this trait. Although patterns of introgression and phylogenetic discordance were heterogenous across the genome, a strong effect of gene density suggests that, in general, natural selection opposes introgression and maintains genetic differentiation in gene-rich genomic regions. Our results highlight the importance of both de novo mutation and introgression as sources of evolutionary change and indicate a role for de novo mutation in driving parallel evolution in adaptive radiations.
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Affiliation(s)
- Benjamin W Stone
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
| | - Carolyn A Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
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5
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Stone BW, Wessinger CA. Ecological diversification in an adaptive radiation of plants: the role of de novo mutation and introgression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.01.565185. [PMID: 37961506 PMCID: PMC10635055 DOI: 10.1101/2023.11.01.565185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations vs. pre-existing variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns of phylogenetic discordance and introgression in Penstemon subgenus Dasanthera, a small and diverse adaptive radiation of plants. We found that magenta hummingbird-adapted flowers have apparently evolved twice from ancestral blue-violet bee-pollinated flowers within this radiation. These shifts in flower color are accompanied by a variety of inactivating mutations to a key anthocyanin pathway enzyme, suggesting that independent de novo loss-of-function mutations underlie parallel evolution of this trait. Although patterns of introgression and phylogenetic discordance were heterogenous across the genome, a strong effect of gene density suggests that, in general, natural selection opposes introgression and maintains genetic differentiation in gene-rich genomic regions. Our results highlight the importance of both de novo mutation and introgression as sources of evolutionary change and indicate a role for de novo mutation in driving parallel evolution in adaptive radiations.
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Affiliation(s)
- Benjamin W. Stone
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
| | - Carolyn A. Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208-3401, USA
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Ålund M, Cenzer M, Bierne N, Boughman JW, Cerca J, Comerford MS, Culicchi A, Langerhans B, McFarlane SE, Möst MH, North H, Qvarnström A, Ravinet M, Svanbäck R, Taylor SA. Anthropogenic Change and the Process of Speciation. Cold Spring Harb Perspect Biol 2023; 15:a041455. [PMID: 37788888 PMCID: PMC10691492 DOI: 10.1101/cshperspect.a041455] [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: 10/05/2023]
Abstract
Anthropogenic impacts on the environment alter speciation processes by affecting both geographical contexts and selection patterns on a worldwide scale. Here we review evidence of these effects. We find that human activities often generate spatial isolation between populations and thereby promote genetic divergence but also frequently cause sudden secondary contact and hybridization between diverging lineages. Human-caused environmental changes produce new ecological niches, altering selection in diverse ways that can drive diversification; but changes also often remove niches and cause extirpations. Human impacts that alter selection regimes are widespread and strong in magnitude, ranging from local changes in biotic and abiotic conditions to direct harvesting to global climate change. Altered selection, and evolutionary responses to it, impacts early-stage divergence of lineages, but does not necessarily lead toward speciation and persistence of separate species. Altogether, humans both promote and hinder speciation, although new species would form very slowly relative to anthropogenic hybridization, which can be nearly instantaneous. Speculating about the future of speciation, we highlight two key conclusions: (1) Humans will have a large influence on extinction and "despeciation" dynamics in the short term and on early-stage lineage divergence, and thus potentially speciation in the longer term, and (2) long-term monitoring combined with easily dated anthropogenic changes will improve our understanding of the processes of speciation. We can use this knowledge to preserve and restore ecosystems in ways that promote (re-)diversification, increasing future opportunities of speciation and enhancing biodiversity.
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Affiliation(s)
- Murielle Ålund
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Meredith Cenzer
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
| | - Nicolas Bierne
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier 34095, France
| | - Janette W Boughman
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - José Cerca
- CEES - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo 0316, Norway
| | | | - Alessandro Culicchi
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Brian Langerhans
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - S Eryn McFarlane
- Department of Botany, University of Wyoming, Laramie, Wyoming 82071, USA
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Markus H Möst
- Research Department for Limnology, University of Innsbruck, Innsbruck 6020, Austria
| | - Henry North
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Anna Qvarnström
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Richard Svanbäck
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80309, USA
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7
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Sapozhnikova YP, Koroleva AG, Yakhnenko VM, Volkova AA, Avezova TN, Glyzina OY, Sakirko MV, Tolstikova LI, Sukhanova LV. Thermal Preconditioning Alters the Stability of Hump-Snout Whitefish ( Coregonus fluviatilis) and Its Hybrid Form, Showing Potential for Aquaculture. BIOLOGY 2023; 12:1348. [PMID: 37887058 PMCID: PMC10603914 DOI: 10.3390/biology12101348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023]
Abstract
One of the little-studied ways that climate warming or temperature increases in aquaculture could affect aquatic animals is through accelerated aging. This study is dedicated to understanding the principles of molecular and cellular aging in the target tissues of juvenile whitefishes (Yenisei hump-snout whitefish and its hybrid) under the influence of acute heat stress (up to 26 °C), and the effects of thermal preconditioning as pre-adaptation. Non-adapted stressed hump-snout whitefish showed a higher induction threshold for functionally active mitochondria in the blood and a decrease in telomerase activity in the liver after heat shock exposure as a long-term compensatory response to prevent telomere shortening. However, we observed heat-induced telomere shortening in non-adapted hybrids, which can be explained by a decrease in mitochondrial membrane stability and a gradual increase in energy demand, leading to a decrease in protective telomerase activity. The pre-adapted groups of hump-snout whitefish and hybrids showed a long-term or delayed response of telomerase activity to heat shock, which served as a therapeutic mechanism against telomere shortening. We concluded that the telomerase and telomere responses to thermal stress demonstrate plasticity of tolerance limits and greater stability in hump-snout whitefish compared with hybrids.
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Affiliation(s)
- Yulia P. Sapozhnikova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya, 664033 Irkutsk, Russia; (V.M.Y.); (A.A.V.); (T.N.A.); (O.Y.G.); (M.V.S.); (L.I.T.); (L.V.S.)
| | - Anastasia G. Koroleva
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya, 664033 Irkutsk, Russia; (V.M.Y.); (A.A.V.); (T.N.A.); (O.Y.G.); (M.V.S.); (L.I.T.); (L.V.S.)
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8
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Short AW, Streisfeld MA. Ancient hybridization leads to the repeated evolution of red flowers across a monkeyflower radiation. Evol Lett 2023; 7:293-304. [PMID: 37829500 PMCID: PMC10565894 DOI: 10.1093/evlett/qrad024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/14/2023] [Accepted: 05/12/2023] [Indexed: 10/14/2023] Open
Abstract
The reuse of old genetic variation can promote rapid diversification in evolutionary radiations, but in most cases, the historical events underlying this divergence are not known. For example, ancient hybridization can generate new combinations of alleles that sort into descendant lineages, potentially providing the raw material to initiate divergence. In the Mimulus aurantiacus species complex, there is evidence for widespread gene flow among members of this radiation. In addition, allelic variation in the MaMyb2 gene is responsible for differences in flower color between the closely related ecotypes of subspecies puniceus, contributing to reproductive isolation by pollinators. Previous work suggested that MaMyb2 was introgressed into the red-flowered ecotype of puniceus. However, additional taxa within the radiation have independently evolved red flowers from their yellow-flowered ancestors, raising the possibility that this introgression had a more ancient origin. In this study, we used repeated tests of admixture from whole-genome sequence data across this diverse radiation to demonstrate that there has been both ancient and recurrent hybridization in this group. However, most of the signal of this ancient introgression has been removed due to selection, suggesting that widespread barriers to gene flow are in place between taxa. Yet, a roughly 30 kb region that contains the MaMyb2 gene is currently shared only among the red-flowered taxa. Patterns of admixture, sequence divergence, and extended haplotype homozygosity across this region confirm a history of ancient hybridization, where functional variants have been preserved due to positive selection in red-flowered taxa but lost in their yellow-flowered counterparts. The results of this study reveal that selection against gene flow can reduce genomic signatures of ancient hybridization, but that historical introgression can provide essential genetic variation that facilitates the repeated evolution of phenotypic traits between lineages.
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Affiliation(s)
- Aidan W Short
- Institute of Ecology and Evolution, 5289 University of Oregon, Eugene, OR 97403-5289, United States
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, 5289 University of Oregon, Eugene, OR 97403-5289, United States
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9
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Cerca J, Cotoras DD, Santander CG, Bieker VC, Hutchins L, Morin-Lagos J, Prada CF, Kennedy S, Krehenwinkel H, Rominger AJ, Meier J, Dimitrov D, Struck TH, Gillespie RG. Multiple paths toward repeated phenotypic evolution in the spiny-leg adaptive radiation (Tetragnatha; Hawai'i). Mol Ecol 2023; 32:4971-4985. [PMID: 37515430 DOI: 10.1111/mec.17082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
The repeated evolution of phenotypes provides clear evidence for the role of natural selection in driving evolutionary change. However, the evolutionary origin of repeated phenotypes can be difficult to disentangle as it can arise from a combination of factors such as gene flow, shared ancestral polymorphisms or mutation. Here, we investigate the presence of these evolutionary processes in the Hawaiian spiny-leg Tetragnatha adaptive radiation, which includes four microhabitat-specialists or ecomorphs, with different body pigmentation and size (Green, Large Brown, Maroon, and Small Brown). We investigated the evolutionary history of this radiation using 76 newly generated low-coverage, whole-genome resequenced samples, along with phylogenetic and population genomic tools. Considering the Green ecomorph as the ancestral state, our results suggest that the Green ecomorph likely re-evolved once, the Large Brown and Maroon ecomorphs evolved twice and the Small Brown evolved three times. We found that the evolution of the Maroon and Small Brown ecomorphs likely involved ancestral hybridization events, while the Green and Large Brown ecomorphs likely evolved through novel mutations, despite a high rate of incomplete lineage sorting in the dataset. Our findings demonstrate that the repeated evolution of ecomorphs in the Hawaiian spiny-leg Tetragnatha is influenced by multiple evolutionary processes.
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Affiliation(s)
- José Cerca
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, Berkeley, California, USA
- Frontiers in Evolutionary Zoology, Natural History Museum, University of Oslo, Oslo, Norway
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Darko D Cotoras
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany
- Department of Entomology, California Academy of Sciences, San Francisco, California, USA
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Leke Hutchins
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, Berkeley, California, USA
| | - Jaime Morin-Lagos
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Carlos F Prada
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Tolima, Colombia
| | - Susan Kennedy
- Department of Biogeography, Trier University, Trier, Germany
| | | | - Andrew J Rominger
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
| | - Joana Meier
- Department of Zoology, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Sanger Institute, Hinxton, UK
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Torsten H Struck
- Frontiers in Evolutionary Zoology, Natural History Museum, University of Oslo, Oslo, Norway
| | - Rosemary G Gillespie
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, Berkeley, California, USA
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10
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Louis M, Korlević P, Nykänen M, Archer F, Berrow S, Brownlow A, Lorenzen ED, O'Brien J, Post K, Racimo F, Rogan E, Rosel PE, Sinding MHS, van der Es H, Wales N, Fontaine MC, Gaggiotti OE, Foote AD. Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters. Nat Commun 2023; 14:4020. [PMID: 37463880 DOI: 10.1038/s41467-023-39532-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats.
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Affiliation(s)
- Marie Louis
- Centre for Biological Diversity, Sir Harold Mitchell Building and Dyers Brae, University of St Andrews, St Andrews, KY16 9TH, Scotland, UK.
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands.
- Greenland Institute of Natural Resources, Kivioq 2, Nuuk, 3900, Greenland.
| | - Petra Korlević
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Milaja Nykänen
- Department of Environmental and Biological Sciences, PO Box 111, FI-80101, Joensuu, Finland
- School of Biological, Earth and Environmental Sciences, University College Cork, North Mall, Cork, Ireland
| | - Frederick Archer
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, NOAA, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Simon Berrow
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Atlantic Technological University, Dublin Road, H91 T8NW, Galway, Ireland
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Eline D Lorenzen
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Joanne O'Brien
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Atlantic Technological University, Dublin Road, H91 T8NW, Galway, Ireland
| | - Klaas Post
- Natural History Museum Rotterdam, Westzeedijk 345, 3015 AA, Rotterdam, Netherlands
| | - Fernando Racimo
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Emer Rogan
- School of Biological, Earth and Environmental Sciences, University College Cork, North Mall, Cork, Ireland
| | - Patricia E Rosel
- Marine Mammal and Turtle Division, Southeast Fisheries Science Center, NOAA, 646 Cajundome Boulevard, Lafayette, LA, 70506, USA
| | - Mikkel-Holger S Sinding
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Henry van der Es
- Natural History Museum Rotterdam, Westzeedijk 345, 3015 AA, Rotterdam, Netherlands
| | - Nathan Wales
- University of York, BioArCh, Environment Building, Wentworth Way, Heslington, York, YO10 5DD, UK
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
- MIVEGEC (Université de Montpellier, CNRS 5290, IRD 229) Institut de Recherche pour le Développement (IRD), F-34394, Montpellier, France
| | - Oscar E Gaggiotti
- Centre for Biological Diversity, Sir Harold Mitchell Building and Dyers Brae, University of St Andrews, St Andrews, KY16 9TH, Scotland, UK
| | - Andrew D Foote
- Department of Natural History, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway.
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316, Oslo, Norway.
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11
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Cerca J, Cotoras DD, Bieker VC, De-Kayne R, Vargas P, Fernández-Mazuecos M, López-Delgado J, White O, Stervander M, Geneva AJ, Guevara Andino JE, Meier JI, Roeble L, Brée B, Patiño J, Guayasamin JM, Torres MDL, Valdebenito H, Castañeda MDR, Chaves JA, Díaz PJ, Valente L, Knope ML, Price JP, Rieseberg LH, Baldwin BG, Emerson BC, Rivas-Torres G, Gillespie R, Martin MD. Evolutionary genomics of oceanic island radiations. Trends Ecol Evol 2023:S0169-5347(23)00032-0. [PMID: 36870806 DOI: 10.1016/j.tree.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023]
Abstract
A recurring feature of oceanic archipelagos is the presence of adaptive radiations that generate endemic, species-rich clades that can offer outstanding insight into the links between ecology and evolution. Recent developments in evolutionary genomics have contributed towards solving long-standing questions at this interface. Using a comprehensive literature search, we identify studies spanning 19 oceanic archipelagos and 110 putative adaptive radiations, but find that most of these radiations have not yet been investigated from an evolutionary genomics perspective. Our review reveals different gaps in knowledge related to the lack of implementation of genomic approaches, as well as undersampled taxonomic and geographic areas. Filling those gaps with the required data will help to deepen our understanding of adaptation, speciation, and other evolutionary processes.
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Affiliation(s)
- José Cerca
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Darko D Cotoras
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Department of Entomology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Rishi De-Kayne
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Pablo Vargas
- Biodiversity and Conservation, Real Jardín Botánico, 28014 Madrid, Spain
| | - Mario Fernández-Mazuecos
- Departamento de Biología (Botánica), Facultad de Ciencias, Universidad Autónoma de Madrid, Calle Darwin 2, 28049 Madrid, Spain; Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid (CIBC-UAM), Calle Darwin 2, 28049 Madrid, Spain
| | - Julia López-Delgado
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Oliver White
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Martin Stervander
- Bird Group, Natural History Museum, Akeman Street, Tring, Hertfordshire HP23 6AP, UK
| | - Anthony J Geneva
- Department of Biology and Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ, USA
| | - Juan Ernesto Guevara Andino
- Grupo de Investigación en Biodiversidad Medio Ambiente y Salud (BIOMAS), Universidad de las Américas, Quito, Ecuador
| | - Joana Isabel Meier
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Lizzie Roeble
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700, 5 CC Groningen, The Netherlands
| | - Baptiste Brée
- Université de Pau et des Pays de l'Adour (UPPA), Energy Environment Solutions (E2S), Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM), 64000 Pau, France
| | - Jairo Patiño
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Calle Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Juan M Guayasamin
- Laboratorio de Biología Evolutiva, Instituto Biósfera, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, 170901 Quito, Ecuador; Galapagos Science Center, Universidad San Francisco de Quito (USFQ) and University of North Carolina (UNC) at Chapel Hill, San Cristobal, Galapagos, Ecuador
| | - María de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, Quito, Ecuador; Galapagos Science Center, Universidad San Francisco de Quito (USFQ) and University of North Carolina (UNC) at Chapel Hill, San Cristobal, Galapagos, Ecuador
| | - Hugo Valdebenito
- Galapagos Science Center, Universidad San Francisco de Quito (USFQ) and University of North Carolina (UNC) at Chapel Hill, San Cristobal, Galapagos, Ecuador; Herbarium of Economic Botany of Ecuador (Herabario QUSF), Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, Quito, Ecuador
| | | | - Jaime A Chaves
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA; Laboratorio de Biología Evolutiva, Instituto Biósfera, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, 170901 Quito, Ecuador
| | - Patricia Jaramillo Díaz
- Estación Científica Charles Darwin, Fundación Charles Darwin, Santa Cruz, Galápagos, Ecuador; Department of Botany and Plant Physiology, University of Málaga, Málaga, Spain
| | - Luis Valente
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700, 5 CC Groningen, The Netherlands
| | - Matthew L Knope
- Department of Biology, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, 96720, HI, USA
| | - Jonathan P Price
- Department of Biology, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, 96720, HI, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Bruce G Baldwin
- Jepson Herbarium and Department of Integrative Biology, 1001 Valley Life Sciences Building 2465, University of California, Berkeley, CA 94720-2465, USA
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna, Spain
| | - Gonzalo Rivas-Torres
- Estación Científica Charles Darwin, Fundación Charles Darwin, Santa Cruz, Galápagos, Ecuador; Estación de Biodiversidad Tiputini, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Rosemary Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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12
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Selz OM, Seehausen O. A taxonomic revision of ten whitefish species from the lakes Lucerne, Sarnen, Sempach and Zug, Switzerland, with descriptions of seven new species (Teleostei, Coregonidae). Zookeys 2023; 1144:95-169. [DOI: 10.3897/zookeys.1144.67747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/22/2022] [Indexed: 02/04/2023] Open
Abstract
The taxonomy of the endemic whitefish of the lakes of the Reuss River system (Lucerne, Sarnen, Zug) and Lake Sempach, Switzerland, is reviewed and revised. Lake Lucerne harbours five species. Coregonus intermundiasp. nov. and C. suspensussp. nov., are described. Coregonus nobilis Haack, 1882, C. suidteri Fatio, 1885, and C. zugensis Nüsslin, 1882, are redescribed. Genetic studies have shown that C. suidteri and C. zugensis are composed of several distinct species endemic to different lakes. The names C. suidteri and C. zugensis are restricted to the species of lakes Sempach and Zug, respectively. The whitefish populations previously referred to as C. suidteri and C. zugensis from Lake Lucerne are described as C. litoralissp. nov. and C. muellerisp. nov., respectively. Furthermore, the whitefish from Lake Zug that were previously referred to as C. suidteri are described as C. supersumsp. nov. A holotype is designated for C. supersum that was previously one of two syntypes of C. zugensis. The other syntype is retained for C. zugensis. Coregonus obliterussp. nov. is described from Lake Zug, and C. obliterus and C. zugensis from Lake Zug are extinct. Finally, we describe C. sarnensissp. nov. from lakes Sarnen and Alpnach. Coregonus suidteri from Lake Sempach shows strong signals of introgression from deliberately translocated non-native whitefish species, which questions if the extant population still carries a genetic legacy from the original species and thus may need to be considered extinct. Coregonus suspensus is genetically partially of allochthonous origin, closely related to the radiation of Lake Constance. It is therefore compared to all known and described species of Lake Constance: C. wartmanni Bloch, 1784, C. macrophthalmus Nüsslin, 1882, C. arenicolus Kottelat,1997, and C. gutturosus Gmelin, 1818.
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13
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Calboli FCF, Iso-Touru T, Bitz O, Fischer D, Nousiainen A, Koskinen H, Tapio M, Tapio I, Kause A. Genomic selection for survival under naturally occurring Saprolegnia oomycete infection in farmed European whitefish Coregonus lavaretus. J Anim Sci 2023; 101:skad333. [PMID: 37777972 PMCID: PMC10583997 DOI: 10.1093/jas/skad333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/29/2023] [Indexed: 10/03/2023] Open
Abstract
Saprolegnia oomycete infection causes serious economic losses and reduces fish health in aquaculture. Genomic selection based on thousands of DNA markers is a powerful tool to improve fish traits in selective breeding programs. Our goal was to develop a single nucleotide polymorphism (SNP) marker panel and to test its use in genomic selection for improved survival against Saprolegnia infection in European whitefish Coregonus lavaretus, the second most important farmed fish species in Finland. We used a double digest restriction site associated DNA (ddRAD) genotyping by sequencing method to produce a SNP panel, and we tested it analyzing data from a cohort of 1,335 fish, which were measured at different times for mortality to Saprolegnia oomycete infection and weight traits. We calculated the genetic relationship matrix (GRM) from the genome-wide genetic data, integrating it in multivariate mixed models used for the estimation of variance components and genomic breeding values (GEBVs), and to carry out Genome-Wide Association Studies for the presence of quantitative trait loci (QTL) affecting the phenotypes in analysis. We identified one major QTL on chromosome 6 affecting mortality to Saprolegnia infection, explaining 7.7% to 51.3% of genetic variance, and a QTL for weight on chromosome 4, explaining 1.8% to 5.4% of genetic variance. Heritability for mortality was 0.20 to 0.43 on the liability scale, and heritability for weight was 0.44 to 0.53. The QTL for mortality showed an additive allelic effect. We tested whether integrating the QTL for mortality as a fixed factor, together with a new GRM calculated excluding the QTL from the genetic data, would improve the accuracy estimation of GEBVs. This test was done through a cross-validation approach, which indicated that the inclusion of the QTL increased the mean accuracy of the GEBVs by 0.28 points, from 0.33 to 0.61, relative to the use of full GRM only. The area under the curve of the receiver-operator curve for mortality increased from 0.58 to 0.67 when the QTL was included in the model. The inclusion of the QTL as a fixed effect in the model increased the correlation between the GEBVs of early mortality with the late mortality, compared to a model that did not include the QTL. These results validate the usability of the produced SNP panel for genomic selection in European whitefish and highlight the opportunity for modeling QTLs in genomic evaluation of mortality due to Saprolegnia infection.
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Affiliation(s)
| | - Terhi Iso-Touru
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| | - Oliver Bitz
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| | - Daniel Fischer
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| | - Antti Nousiainen
- Natural Resources Institute Finland (LUKE), FI-70210 Kuopio, Finland
| | - Heikki Koskinen
- Natural Resources Institute Finland (LUKE), FI-70210 Kuopio, Finland
| | - Miika Tapio
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| | - Ilma Tapio
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| | - Antti Kause
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
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14
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Stubbs RL, Theodoridis S, Mora‐Carrera E, Keller B, Yousefi N, Potente G, Léveillé‐Bourret É, Celep F, Kochjarová J, Tedoradze G, Eaton DAR, Conti E. Whole-genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot. THE NEW PHYTOLOGIST 2023; 237:656-671. [PMID: 36210520 PMCID: PMC10099377 DOI: 10.1111/nph.18525] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Biodiversity hotspots, such as the Caucasus mountains, provide unprecedented opportunities for understanding the evolutionary processes that shape species diversity and richness. Therefore, we investigated the evolution of Primula sect. Primula, a clade with a high degree of endemism in the Caucasus. We performed phylogenetic and network analyses of whole-genome resequencing data from the entire nuclear genome, the entire chloroplast genome, and the entire heterostyly supergene. The different characteristics of the genomic partitions and the resulting phylogenetic incongruences enabled us to disentangle evolutionary histories resulting from tokogenetic vs cladogenetic processes. We provide the first phylogeny inferred from the heterostyly supergene that includes all species of Primula sect. Primula. Our results identified recurrent admixture at deep nodes between lineages in the Caucasus as the cause of non-monophyly in Primula. Biogeographic analyses support the 'out-of-the-Caucasus' hypothesis, emphasizing the importance of this hotspot as a cradle for biodiversity. Our findings provide novel insights into causal processes of phylogenetic discordance, demonstrating that genome-wide analyses from partitions with contrasting genetic characteristics and broad geographic sampling are crucial for disentangling the diversification of species-rich clades in biodiversity hotspots.
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Affiliation(s)
- Rebecca L. Stubbs
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Spyros Theodoridis
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F)Frankfurt am Main60325Germany
| | - Emiliano Mora‐Carrera
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Barbara Keller
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Narjes Yousefi
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Giacomo Potente
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Étienne Léveillé‐Bourret
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV)Université de MontréalQuébecH1X 2B2Canada
| | - Ferhat Celep
- Department of Biology, Faculty of Arts and SciencesKırıkkale UniversityKırıkkale71450Turkey
| | - Judita Kochjarová
- Department of Phytology, Faculty of ForestryTechnical University in ZvolenZvolen96001Slovak Republic
| | - Giorgi Tedoradze
- Department of Plant Systematics and Geography, Institute of BotanyIlia State UniversityTbilisi0105Georgia
| | - Deren A. R. Eaton
- Department of Ecology, Evolution and Environmental BiologyColumbia UniversityNew YorkNY10027USA
| | - Elena Conti
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
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15
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Bastide H, López-Villavicencio M, Ogereau D, Lledo J, Dutrillaux AM, Debat V, Llaurens V. Genome assembly of 3 Amazonian Morpho butterfly species reveals Z-chromosome rearrangements between closely related species living in sympatry. Gigascience 2022; 12:giad033. [PMID: 37216769 PMCID: PMC10202424 DOI: 10.1093/gigascience/giad033] [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: 10/25/2022] [Revised: 02/13/2023] [Accepted: 05/12/2023] [Indexed: 05/24/2023] Open
Abstract
The genomic processes enabling speciation and species coexistence in sympatry are still largely unknown. Here we describe the whole-genome sequencing and assembly of 3 closely related species from the butterfly genus Morpho: Morpho achilles (Linnaeus, 1758), Morpho helenor (Cramer, 1776), and Morpho deidamia (Höbner, 1819). These large blue butterflies are emblematic species of the Amazonian rainforest. They live in sympatry in a wide range of their geographical distribution and display parallel diversification of dorsal wing color pattern, suggesting local mimicry. By sequencing, assembling, and annotating their genomes, we aim at uncovering prezygotic barriers preventing gene flow between these sympatric species. We found a genome size of 480 Mb for the 3 species and a chromosomal number ranging from 2n = 54 for M. deidamia to 2n = 56 for M. achilles and M. helenor. We also detected inversions on the sex chromosome Z that were differentially fixed between species, suggesting that chromosomal rearrangements may contribute to their reproductive isolation. The annotation of their genomes allowed us to recover in each species at least 12,000 protein-coding genes and to discover duplications of genes potentially involved in prezygotic isolation like genes controlling color discrimination (L-opsin). Altogether, the assembly and the annotation of these 3 new reference genomes open new research avenues into the genomic architecture of speciation and reinforcement in sympatry, establishing Morpho butterflies as a new eco-evolutionary model.
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Affiliation(s)
| | - Manuela López-Villavicencio
- Institut de Systématique, Evolution et Biodiversité (UMR 7205 CNRS/MNHN/SU/EPHE/UA), Muséum National d’Histoire Naturelle–CP50, 75005 Paris, France
| | | | - Joanna Lledo
- GeT-PlaGe, Bât G2, INRAe, 31326 Castanet-Tolosan Cedex, France
| | - Anne-Marie Dutrillaux
- Institut de Systématique, Evolution et Biodiversité (UMR 7205 CNRS/MNHN/SU/EPHE/UA), Muséum National d’Histoire Naturelle–CP50, 75005 Paris, France
| | - Vincent Debat
- Institut de Systématique, Evolution et Biodiversité (UMR 7205 CNRS/MNHN/SU/EPHE/UA), Muséum National d’Histoire Naturelle–CP50, 75005 Paris, France
| | - Violaine Llaurens
- Institut de Systématique, Evolution et Biodiversité (UMR 7205 CNRS/MNHN/SU/EPHE/UA), Muséum National d’Histoire Naturelle–CP50, 75005 Paris, France
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